Re: [Freesurfer] Getting combined bvals/bvecs
Hi Marissa - You have to specify as many b-values and gradient vectors as there are volumes in your DWI data file. This means that, if you combine the AP and PA volumes, you also have to concatenate the bvals from the two into one file, and do the same with the bvecs. Make sure that the order in which the AP and PA volumes are combined is the same as the order in which the corresponding bvals and bvecs are combined. Hope this helps, a.y On Wed, 14 Sep 2016, Marissa Pifer wrote: Hello freesurfer experts, I am trying to run tracula on subjects that have separate AP/PA direction DTI files. We combined the data into one using topup, and would now like to run tracula on the subject. The problem is, the combined file doesn't have a bvals/bvecs file. When I try to use the original bval/bvec files, I get the error that the bvals and bvecs don't match up. I have tried combining the files into one, and then running a dicom to nifty conversion to get a combined bvals/bvecs output, but that results again in two separate bvals/bvecs files as well. I then tried just have two specified bvals and bvecs. This did not give us an error message, but trac-prep took only a few seconds and did not complete the steps it was supposed to to create the directories for trac-bedp to complete. I have attached our dmrirc.example file and the log for the trac-prep step for your reference. The questions then are; is there a way to get one bvals/bvecs file that has the correct parameters for the AP and PA combined file. Or, if not, is there a way to run tracula with two sets of bvals and bvecs (one for the AP and one for the PA direction)? In case you need this information, the process is being run with freesurfer 5.3, on a macbook pro OS X version 10.9.5. Thank you in advance, Marissa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula movement
You're right that this looks fine. Can you upload the entire DWI series for me here? Nifti is fine. Thanks! https://gate.nmr.mgh.harvard.edu/filedrop2/ On Mon, 12 Sep 2016, Lars M. Rimol wrote: Re: [Freesurfer] Tracula movement Anastasia Yendiki Mon, 12 Sep 2016 04:24:56 -0700 Hi Lars - This sounds like the subject was trying to climb out of the scanner: 3cm average translational motion and 24% of the slices in the series have drop-out. How do the images look? a.y Hi, I don't have a lot of experience looking at dwi scans, but they don't seem crazy to me. I have attached screenshots of the dwi, FA, and brain_anat_mni images, and the gross anatomy looks fine to me. There are stripes in brain_anat_mni, which I would guess indicate motion.. Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula movement
Hi Lars - This sounds like the subject was trying to climb out of the scanner: 3cm average translational motion and 24% of the slices in the series have drop-out. How do the images look? a.y On Mon, 12 Sep 2016, Lars M. Rimol wrote: HI, Is there a rule-of-thumb upper level of acceptable head motion? The tutorial gives these values as examples: AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore 0.489419 0.00398925 0 1 I have a subject with AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore 30.018 0.209 24 1.6 I plan, of course, to use the index described in Yendiki et al. (2013) but would such high levels nevertheless be considered disqualifying a priori? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
Good to know, thanks for sharing this trick! On Sat, 3 Sep 2016, Chung, Yoonho wrote: I found out why it didn't work. One of the script that bedpostx_postproc.sh calls is written in python2. I set my default to python3 and therefore caused the error in the last step. After I loaded python2 environment, i got the merged files and finished properly. Thanks for your help as always! Yoon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all -bedp ERROR: Could not read - merged_ph1samples.nii.gz
Hi Yoon - It sounds like FSL's bedpostx postprocessing script failed. You can run it like this: bedpostx_postproc.sh /path/to/your/subject/dmri This script merges the results from all the slices. It's possible that something went wrong with the slices (you ran out disk space for example). If the slice results are ok, this'll do it. Best, a.y On Fri, 2 Sep 2016, Chung, Yoonho wrote: Hi Anastasia, trac-all -prep completed without error. I thought trac-all -bedp starts and ends without any error but trac-all path failed with these messages. Loading BEDPOST parameter samples from */dmri.bedpostX niiRead(): error opening file*/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read */dmri.bedpostX/merged_ph1samples.nii.gz I looked at the dmri.bedpostX directory and all slices exist in the dmri.bedpostX/diff_slices directory but realized the trac-all -bedp phase did not create the merged samples in this directory. I am currently runnning with FSL/5.0.6 Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ and freesurfer version 5.3 I looked through the mailing list to see if someone ran into a similar problem but could not find a good solution. Do you have what may have caused this? Any other files I would like to look into? Thank you Yoon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula Error -preproc Segmentation fault (core dumped)
Hi Kristina - I suspect there's some misregistration, or part of the brain mask (and hence the anatomical segmentation) missing or something like that. Do you mind uploading the tracula directories of this subject for me to take a look at? https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y On Thu, 1 Sep 2016, Kristina Jelinkova wrote: Hello everyone, I've been using Tracula for a while now with much success (and help from the archive) but I've run into an error I haven't been able to solve. I have several subjects for which trac-all -preproc ends with Segmentation fault (core dumped) I don't think it's a mistake with my directories, they appear correct and I've ran numerous subjects successfully like this already. The dti data and aparc+aseg also appear normal. I'm attaching the trac-all log and error log from one of these problematic subjects. Any insight would be greatly appreciate! Thank you, Kristina Jelinkova ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] About TRACULA results
Hi there - If you upload the tracula directories for me, I'm happy to try to figure out what's going on. Although honestly at this point it's worth waiting for the new version. Thanks! a.y On Tue, 30 Aug 2016, Kang, XJ wrote: Hi, I am trying to computer the changes of cortical parcellations and fiber pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I copied the anatomical and DWI images from the same scan session into five directories. Run recon-all and trac-all on the 5 same data sets, in order to check the reproducibility of the analysis. Here are what I got: the Desikan-Killiany parcellations in both GM and WM, and the subcortical structures, repeat well. No difference found in volume or size of those structures. However, the volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, varies for the 5 sets. tracula.conf files were copied from ~/freesurfer/bin/dmrirc.example. The changes are calculated in percentage by (S1-S0)/((S1+S0)/2)*100%. For example, the changes of averaged FA between the 5 data sets are : ?? ? S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , -1.1 , 6.0 , 0.5 , 1.3 , Corpus Callosum - Forceps Minor , 0.1 , 0.0 , -1.6 , 0.0 , Right Anterior Thalamic Radiations , 0.1 , -1.0 , 0.5 , 0.9 , Right Cingulum - Angular Bundle , -4.8 , -2.0 , -1.5 , 3.8 , Right Cingulum - Cingulate Gyrus Endings , 0.5 , -0.9 , 0.4 , -2.3 , Right Corticospinal Tract , 1.9 , 0.6 , -2.2 , 1.4 , Right Inferior Longitudinal Fasciculus , -2.2 , -0.8 , -1.3 , 3.0 , Right Superior Longitudinal Fasciculus - Parietal Endings , 0.8 , -0.4 , -1.2 , 0.2 , Right Superior Longitudinal Fasciculus - Temporal Endings , -4.9 , -0.6 , -2.6 , -1.3 , Right Uncinate Fasciculus , 0.5 , 1.6 , -0.9 , 3.5 , Even larger changes for the volume of the pathways: ?? ? S1-S0, S2-S0, S3-S0, S4-S0 Corpus Callosum - Forceps Major , 2.2 , -33.7 , -12.3 , 1.1 , Corpus Callosum - Forceps Minor , 11.9 , 4.8 , 0.6 , 7.2 , Right Anterior Thalamic Radiations , -8.9 , 2.2 , -12.5 , 7.5 , Right Cingulum - Angular Bundle , -38.1 , 41.6 , 34.8 , 8.6 , Right Cingulum - Cingulate Gyrus Endings , 24.4 , 33.1 , 21.3 , 17.5 , Right Corticospinal Tract , 9.8 , -3.0 , 2.2 , 19.5 , Right Inferior Longitudinal Fasciculus , 7.2 , 24.1 , -7.3 , 23.8 , Right Superior Longitudinal Fasciculus - Parietal Endings , 17.2 , 10.2 , 25.1 , 9.9 , Right Superior Longitudinal Fasciculus - Temporal Endings , 15.4 , 3.4 , -3.1 , -11.5 , Right Uncinate Fasciculus , 13.3 , -1.2 , 16.4 , -3.4 , Any expert has the experience on these? Thank you for your help. XJ Kang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Satellite Symposia - Resting-State and Brain Connectivity Conference
Dear FreeSurfers - If you're attending the Resting-State and Brain Connectivity Conference in Vienna, you can now register for satellite symposia, including one on diffusion MRI. Hope to see you there! a.y -- We are pleased to inform you that registration for the six Satellite Symposia at the Resting-State and Brain Connectivity Conference is open! These specialised meetings will take place on Saturday, September 24th right after the Resting-State and Brain Connectivity Conference. So why not extend your stay in Vienna for the sake of maximizing knowledge gain, deepening the vivid scientific exchange and socializing with your community members? The Satellite Symposia will will cover diffusion MRI, optogenetics, PET/MRI, TMS/fMRI and predictive analyses of neuroimaging data. We made sure to provide a large selection of topics for our six Satellite Symposia, so that everyone gets to choose the most interesting on their behalf: * Symposium #1: Probing white-matter anatomy and microstructure with diffusion MRI * Symposium #2: Tackling connectivity using non-invasive brain stimulation (fMRI/TMS, tDCS, tACS) * Symposium #3: The Emerging Field of Predictive Analytics in Neuroimaging: Applications, Challenges and Perspectives * Symposium #4: Multi-modal fMRI from photons to protons * Symposium #5: Dynamic Functional Connectivity * Symposium #6: Network-Based Approaches for Neuroimaging: Graph Theory Techniques for Brain Connectivity Research http://www.restingstate.com/2016/satellite-symposia/ So don’t hesitate to register for a satellite symposium now! We look forward to welcoming you to Vienna in September 2016! On behalf of the local and international organizing committees Christian Windischberger Claus Lamm Rupert Lanzenberger Bharat Biswal Mark Lowe Christopher Pawela Martin Walter Susan Whitfield-Gabrieli___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat
No need to rerun anything. It's an issue with the format of those mean path files. Just view them in the standard 5.3 version of freeview for now. On Fri, 26 Aug 2016, Elijah Mak wrote: Hi Anastasia, Yes indeed. I am using a dev version of freeview. I could give it another go with the freeview that came with v5.3. But does this mean that I shoudl also I re-run the tracula -stat on a v5.3? Thanks! Best Wishes, Elijah ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat
Hi Elijah - Glad to hear that things worked out! Are you by any chance using the dev version of freeview? a.y On Fri, 26 Aug 2016, Elijah Mak wrote: Hi Anastasia and others, I am trying to visualise the *.path.mean.txt on MNI template after running trac-all -stat. I used this command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w stats/*.path.mean.txt However, it looks like something has gone wrong with the labelling and position of the tracts (note the CST highlighted in green). https://www.dropbox.com/s/ndpkfgbrfgvt5q1/Screen%20Shot%202016-08-22%20at%2014.41.37.png?dl=0 Everything was fine and correctly labelled when I checked the merged tracks. Thanks again for your help! Best Wishes, Elijah P.S. On another note, the reinit=1 trick works very well and I was able to reconstruct the tracts in almost all cases. Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] wmparc parcellation for thalamus and brainstem
Hi Vasudev - These regions are part of the subcortical segmentation (aseg) volume: http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI a.y On Thu, 25 Aug 2016, Dev vasu wrote: Dear all, After running through recon-all ,I have obtained wmparc parcellation file (see the attached figure ). I would like to obtain parcellation at specific regions of interest for my study i.e Brain stem region and Thalamus region, could you please let me know how i could perform parcellation for these two specific regions of interest ( i.e. Brain stem and Thalamus ). Thanks Vasudev ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] dmri_poistats
Hi Mohamad - This tool hasn't been worked on for over a decade, and there is nobody here who can support it. There are tools out there that do tractography without anatomical priors (in fact that's approximately all the tools out there), but none in freesurfer at the moment. Best, a.y On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote: Hi Anastasia, This tool is available in (FS 5.3 and FS v6.0) as version 1.0 Beta. But in the paper that I have pointed to, the folks used the version 1.4 of this tool. That's why I am a bit confused. Kindly, are there any tools that can help to do tractography for the corticospinal tract when T1 images are not available? Thank you for any advice Mohamad -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki Sent: Wednesday, August 24, 2016 10:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] dmri_poistats Hi Mohamad - This tool is *way* deprecated. It should not have been included in beta releases. Thanks for bringing this to our attention. a.y On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote: Dear Freesurfer experts, I would like to inquire about the tool “dmri_poistats” https://surfer.nmr.mgh.harvard.edu/fswiki/PoistatsOverview. This tool is included as a beta release ( in FS5.3 and FS 6.0). In literature review I found colleagues used the version 1.4 of this tool. e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780023/ Kindly, I have the following two questions: 1. What is the final release of this tool? 2. I have DWI images and no T1 images are available. Is it reliable to do tractography for the corticospinal tract using this tool? Thank you for any advice! Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] dmri_poistats
Hi Mohamad - This tool is *way* deprecated. It should not have been included in beta releases. Thanks for bringing this to our attention. a.y On Wed, 24 Aug 2016, Alshikho, Mohamad J. wrote: Dear Freesurfer experts, I would like to inquire about the tool “dmri_poistats” https://surfer.nmr.mgh.harvard.edu/fswiki/PoistatsOverview. This tool is included as a beta release ( in FS5.3 and FS 6.0). In literature review I found colleagues used the version 1.4 of this tool. e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780023/ Kindly, I have the following two questions: 1. What is the final release of this tool? 2. I have DWI images and no T1 images are available. Is it reliable to do tractography for the corticospinal tract using this tool? Thank you for any advice! Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA: narrow probability distributions
Yes, it shouldn't hurt. On Tue, 23 Aug 2016, Harms, Michael wrote: Ok. We’ll give it a try. Just to confirm, you're agreeing that increasing nburnin and nsample is a “good” thing, right? (e.g., 1000, and 15000, respectively?) If anything, we should be less likely to get narrow tracts when using larger nburnin/nsample values, right? thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 8/23/16, 5:09 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Michael - Even if it starts very close to the true max of the distribution, in practice it'll never stay put. MCMC will accept a new sample path with probability 1 if the new sample has greater probability than the previous sample, and it will also accept it with some very small probability if it doesn't. This means that it'll still explore the space around the max, even if it ends up returning to the max pretty quickly. So most likely there's something weird about the initial path if it doesn't move at all. Best, a.y On Tue, 23 Aug 2016, Harms, Michael wrote: Hi Anastasia, My interpretation of the “reinit” parameter is that it is for situations where a narrow probability distribution is assumed to be incorrect. But how do you know whether it is indeed incorrect, or whether in fact the true equilibrium distribution is (correctly) very narrow? In particular, my understanding of MCMC is that higher burn-in, and more sampling iterations are only a “good” thing. i.e., If we have the time and compute resources, we shouldn’t hesitate to increase them from their defaults, to help to make sure we are capturing the true equilibrium distribution. So, if increasing the nburnin and nsample values makes it more likely to find spatially narrow tract distributions, isn’t that a sign that the true distribution should indeed be narrow? thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 8/23/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Dillan - There's a work-around for this, see the reinit variable at the bottom of the sample config file: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc I'm hoping to make this happen automatically soon! Best, a.y On Tue, 23 Aug 2016, Newbold, Dillan wrote: Dear Anastasia, I’ve been looking at a lot of Tracula path.pd files and I’ve found that some probability distributions are only a single voxel wide, similar to the path.map file. The few none-zero voxels in these path.pd files have very high probability values. When an isosurface is generated for these tracts, it looks like a short thin blob somewhere in the usual tract distribution. I’ve seen descriptions in the archives of similar “short thin tracts,” but, from what I have seen, no one has offered a satisfying explanation for why these occur. What I think is happening in these tracts is that a maximum-probability (or local maximum) path is found during a burn-in iteration and all following perturbations of that path are rejected. Since the probability value in the path.pd is equal to the number of sample paths intersecting that voxel, finding a local maximum early on results in a small number of very high-probability voxels. Consistent with this explanation, I’ve found that this issue occurs more frequently when nburnin is set to 1000 (default = 200). A similar issue can occur if a local maximum is found early during the sample iterations, and this results in a path.pd file containing a small number of voxels with very high values surrounded by a larger area of low-value voxels. When a 20% threshold is applied, the result is the same as when a local maximum occurs during a burn-in iteration. Does my understanding of this issue seem correct? None of this would be a problem if my only aim were to find the single path with the maximum a posteriori probability, but I’m concerned that the average and weighted_average sats for these tracts will be less accurate. Since these distributions include small fractions of the number of voxels included in most tract distributions, is it likely that the average and weighted_average stats from these narrow distributions are less representative of the whole tract and more subject to random noise? Given these concerns, what type of overall path statistics do you think is most descriptive of a tract? Also, do you feel that higher nburnin and nsample val
Re: [Freesurfer] TRACULA: narrow probability distributions
Hi Michael - Even if it starts very close to the true max of the distribution, in practice it'll never stay put. MCMC will accept a new sample path with probability 1 if the new sample has greater probability than the previous sample, and it will also accept it with some very small probability if it doesn't. This means that it'll still explore the space around the max, even if it ends up returning to the max pretty quickly. So most likely there's something weird about the initial path if it doesn't move at all. Best, a.y On Tue, 23 Aug 2016, Harms, Michael wrote: Hi Anastasia, My interpretation of the “reinit” parameter is that it is for situations where a narrow probability distribution is assumed to be incorrect. But how do you know whether it is indeed incorrect, or whether in fact the true equilibrium distribution is (correctly) very narrow? In particular, my understanding of MCMC is that higher burn-in, and more sampling iterations are only a “good” thing. i.e., If we have the time and compute resources, we shouldn’t hesitate to increase them from their defaults, to help to make sure we are capturing the true equilibrium distribution. So, if increasing the nburnin and nsample values makes it more likely to find spatially narrow tract distributions, isn’t that a sign that the true distribution should indeed be narrow? thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 8/23/16, 4:44 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Dillan - There's a work-around for this, see the reinit variable at the bottom of the sample config file: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc I'm hoping to make this happen automatically soon! Best, a.y On Tue, 23 Aug 2016, Newbold, Dillan wrote: Dear Anastasia, I’ve been looking at a lot of Tracula path.pd files and I’ve found that some probability distributions are only a single voxel wide, similar to the path.map file. The few none-zero voxels in these path.pd files have very high probability values. When an isosurface is generated for these tracts, it looks like a short thin blob somewhere in the usual tract distribution. I’ve seen descriptions in the archives of similar “short thin tracts,” but, from what I have seen, no one has offered a satisfying explanation for why these occur. What I think is happening in these tracts is that a maximum-probability (or local maximum) path is found during a burn-in iteration and all following perturbations of that path are rejected. Since the probability value in the path.pd is equal to the number of sample paths intersecting that voxel, finding a local maximum early on results in a small number of very high-probability voxels. Consistent with this explanation, I’ve found that this issue occurs more frequently when nburnin is set to 1000 (default = 200). A similar issue can occur if a local maximum is found early during the sample iterations, and this results in a path.pd file containing a small number of voxels with very high values surrounded by a larger area of low-value voxels. When a 20% threshold is applied, the result is the same as when a local maximum occurs during a burn-in iteration. Does my understanding of this issue seem correct? None of this would be a problem if my only aim were to find the single path with the maximum a posteriori probability, but I’m concerned that the average and weighted_average sats for these tracts will be less accurate. Since these distributions include small fractions of the number of voxels included in most tract distributions, is it likely that the average and weighted_average stats from these narrow distributions are less representative of the whole tract and more subject to random noise? Given these concerns, what type of overall path statistics do you think is most descriptive of a tract? Also, do you feel that higher nburnin and nsample values should lead to superior results? I would have thought this to be the case, but now it seems to me that setting either of these values too high will result in narrow probability distributions and bad statistics. Thank you, Dillan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibi
Re: [Freesurfer] TRACULA: narrow probability distributions
Hi Dillan - There's a work-around for this, see the reinit variable at the bottom of the sample config file: http://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc I'm hoping to make this happen automatically soon! Best, a.y On Tue, 23 Aug 2016, Newbold, Dillan wrote: Dear Anastasia, I’ve been looking at a lot of Tracula path.pd files and I’ve found that some probability distributions are only a single voxel wide, similar to the path.map file. The few none-zero voxels in these path.pd files have very high probability values. When an isosurface is generated for these tracts, it looks like a short thin blob somewhere in the usual tract distribution. I’ve seen descriptions in the archives of similar “short thin tracts,” but, from what I have seen, no one has offered a satisfying explanation for why these occur. What I think is happening in these tracts is that a maximum-probability (or local maximum) path is found during a burn-in iteration and all following perturbations of that path are rejected. Since the probability value in the path.pd is equal to the number of sample paths intersecting that voxel, finding a local maximum early on results in a small number of very high-probability voxels. Consistent with this explanation, I’ve found that this issue occurs more frequently when nburnin is set to 1000 (default = 200). A similar issue can occur if a local maximum is found early during the sample iterations, and this results in a path.pd file containing a small number of voxels with very high values surrounded by a larger area of low-value voxels. When a 20% threshold is applied, the result is the same as when a local maximum occurs during a burn-in iteration. Does my understanding of this issue seem correct? None of this would be a problem if my only aim were to find the single path with the maximum a posteriori probability, but I’m concerned that the average and weighted_average sats for these tracts will be less accurate. Since these distributions include small fractions of the number of voxels included in most tract distributions, is it likely that the average and weighted_average stats from these narrow distributions are less representative of the whole tract and more subject to random noise? Given these concerns, what type of overall path statistics do you think is most descriptive of a tract? Also, do you feel that higher nburnin and nsample values should lead to superior results? I would have thought this to be the case, but now it seems to me that setting either of these values too high will result in narrow probability distributions and bad statistics. Thank you, Dillan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula ROI analysis CVS vs MNI reg
Hi Yoon - The wmparc and aseg ROIs are in the subject's native T1 space, so you don't need to register across subjects to get ROI-based diffusion measures. You just need to register between the subject's own T1 and DWIs - the recommended method for that is bbregister. You can find more in the multimodal tutorial on the freesurfer wiki. Best, a.y On Tue, 23 Aug 2016, Chung, Yoonho wrote: > > Hi Anastasia, > > > Is there a preferable method between CVS vs MNI registration when extracting > diffusion mesures from ROIs (white matter, ASEG etc)? > > > Best, > > Yoon > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
Hi Elijah - Does the directory in the error message exist? a.y On Fri, 19 Aug 2016, Elijah Mak wrote: Hi Anastasia, The error message occurs for other control points too, but it does not kill the -prior stage. I have attached the full trac-all.log file. This error message is also found in other subjects where I am struggling to get a good initialisation. The ERROR: fio_pushd:subject/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri Thank you! Best Wishes, Elijah -- Elijah Mak PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
Hi Elijah - This error occurs with one number of control points but not another? That would be very strange. I'd have to look at the full trac-al.log to figure it out, I can't guess what's going on just from this one line unfortunately. a.y On Fri, 19 Aug 2016, Elijah Mak wrote: Hi Anastasia, Thanks, it works, but only for MNI reg option. For the CVS stream, there was an error message during -prior. ERROR: fio_pushd: /Users/MacPro/Documents/22995_EM/dmri/xfms/cvs/final_CVSmorph_tocvs_avg35/mri This error message did not halt the process though. Could this be a clue? Thanks for your patience :) Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
Mmm, it sounds like the shape of the tract is too convoluted for it to find a good fit. I'd try increasing the # of control points. On Fri, 19 Aug 2016, Elijah Mak wrote: Hi Anastasia, Thank you for looking into that subject. I have tried reinitiliasation a few times and in all cases, it just could not find a satisfactory control point fit during the -prior stage. Therefore, the -prior stage has been running for more than 10 hours now. This occurs in other a small number of other subjects as well. WARN: Could not find satisfactory control point fit - try 596 How can I resolve this? And what type of problem could be reflected by this? Bad aparc+aseg.mgz / registration to template? If all else fails, I will exclude subjects using the criteria that you set in the Neuroimage paper: where a subject was excluded if there were failures of reconstruction in 2 or more WM tracts. Thank you for your help! Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
Hi Elijah - It looks to me like the forceps major had the same problem for both MNI and CVS in this subject, right? This subject has a relatively thin and somewhat convoluted forceps major, so you can try increasing the number of control points, say from 7 to 8. (But I'd try reinitialization first, before changing anything.) Hope this helps, a.y On Thu, 18 Aug 2016, Elijah Mak wrote: Dear Anastasia, I have also uploaded the file with the problem (22995_EM.zip), and this is how my config file looks like after modifications: set subjlist = (22995) set pathlist = (fmajor_PP) set ncpts = (7) set reinit = (1) Thanks again! Best Wishes, Elijah -- Elijah Mak PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Projecting FA map onto fsaverge surface
Hi Taha - Once you've mapped from the volume onto the white surface, you should be able to display it on the inflated surface, and also to get thickness statistics (thickness is just the distance between corresponding points on the white and pial surface). You don't need to do anything to map from white to inflated within an individual. Best, a.y On Fri, 19 Aug 2016, Taha Abdullah wrote: Excellent! Thank you for the quick advice, I tried this initially but I was using the wrong xfm format. Since I have the FA map in subject ?h.white space, I have done the same with the tract endings too. I am having some difficulties conceptually, in terms of projecting the end points onto either the subject specfic or fsaverage inflated surface. I assumed using mri_surf2surf would be sufficient to transform the endpts from subject surface ?h.white space to the inflated surface, but it is a scalar data file. Once the endpts are projected onto the inflated surface it seems straightforward to extract the thickness values for further analysis. Essentially replicating the attached image from Sølsnesa 2015. If you have any suggestions that would be much appreciated. Thank you very much! Best, Taha On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki wrote: Hi Taha - Trying getting a .dat registration file from bbregister and using that as the input to mri_vol2surf. There's a multimodal tutorial on the freesurfer wiki that might be of help. Best, a.y On Thu, 18 Aug 2016, Taha Abdullah wrote: Hello All, I am trying to project FA map (dtifit_FA.nii.gz) and the endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface space. I was following instructions on http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html, under FreeSurfer Registration, to create the various xfms files. Next, I registered the FA map to subject conformed space using flirt * flirt -in dtifit_FA.nii.gz -ref ../../mri/orig.nii.gz -applyxfm -init ./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz Then, I used mri_vol2surf to project the registered FA map onto fsaverage surface with the following command. * mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 --cortex --hemi rh --trgsubject fsaverage --regheader taha_brain --reg ./xfms_taha/fa2freesurfer.mat --o FA_2fsavg_surf.mgh Upon viewing in freeview the fsavg rh.white surface and fa2FS.nii.gz (FA map in FreeSurfer space) did not allign properly. I have tried some variations wtihout any luck. I used the following command line for freeview. * freeview -f/usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.m gh -v fa2FS.nii.gz * Attached are some pics of the FA confomred map and fsaverage.rh.white surface Do I need a xfm file for taliarch allignment? Any advice or insight would be greatly appreciated. Thanks in advance, Taha Terminal output: from mri_vol2surf srcvol = fa2FS.nii.gz srcreg = ./xfms_taha/fa2freesurfer.mat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjDist = 0.5 reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/taha_brain/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 6 6 6 using old Done mapping volume to surface Number of source voxels hit = 81606 Reading source surface registration /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg Done loading source registration surface Reading target registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (taha_brain -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2
Re: [Freesurfer] red and blue gradient color map for freeview
Hi Eun Young - Not sure if anyone has a more elegant solution but it sounds like you could split your positive and negative activations into 2 volumes and use the 2 different colormaps for them. Best, a.y On Thu, 18 Aug 2016, Eun Young Choi wrote: > Hi all, > > I'd like to have a freeview color map that has both a red-yellow gradient and > a blue-light blue gradient (the typical > colors for positive and negative fcMRI correlations) and ideally no color for > 0... None of the standard color maps in > freeview work well and I can't seem to find one online. Has anyone created > one? Or know where I can view the text file > for the standard color maps that come with freeview, so I can create one > myself? > > Thank you! > Eun Young > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Projecting FA map onto fsaverge surface
Hi Taha - Trying getting a .dat registration file from bbregister and using that as the input to mri_vol2surf. There's a multimodal tutorial on the freesurfer wiki that might be of help. Best, a.y On Thu, 18 Aug 2016, Taha Abdullah wrote: Hello All, I am trying to project FA map (dtifit_FA.nii.gz) and the endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface space. I was following instructions on http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html, under FreeSurfer Registration, to create the various xfms files. Next, I registered the FA map to subject conformed space using flirt * flirt -in dtifit_FA.nii.gz -ref ../../mri/orig.nii.gz -applyxfm -init ./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz Then, I used mri_vol2surf to project the registered FA map onto fsaverage surface with the following command. * mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 --cortex --hemi rh --trgsubject fsaverage --regheader taha_brain --reg ./xfms_taha/fa2freesurfer.mat --o FA_2fsavg_surf.mgh Upon viewing in freeview the fsavg rh.white surface and fa2FS.nii.gz (FA map in FreeSurfer space) did not allign properly. I have tried some variations wtihout any luck. I used the following command line for freeview. * freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.mgh -v fa2FS.nii.gz * Attached are some pics of the FA confomred map and fsaverage.rh.white surface Do I need a xfm file for taliarch allignment? Any advice or insight would be greatly appreciated. Thanks in advance, Taha Terminal output: from mri_vol2surf srcvol = fa2FS.nii.gz srcreg = ./xfms_taha/fa2freesurfer.mat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjDist = 0.5 reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/taha_brain/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 6 6 6 using old Done mapping volume to surface Number of source voxels hit = 81606 Reading source surface registration /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg Done loading source registration surface Reading target registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (taha_brain -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (143161) Reverse Loop had 26084 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 107182, nSrcLost = 0, nSrcMulti = 35979, MnSrcMultiHits = 2.29979 nTrg121 = 142955, nTrgMulti = 20887, MnTrgMultiHits = 2.24882 Masking with /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label Writing to FA_2fsavg_surf.mgh Dim: 163842 1 1 -- Taha Abdullah Department of Physiology Northwestern University Feinberg School of Medicine Masters of Science Physiology and Biophysics, Georgetown University 2015 Work: (312)-503-0413 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
Hi Elijah - You add "set reinit =1" to the config file, (and remember to set the pathlist and subjlist to only what you want to rerun), and then rerun the -prior and -path steps in that order. Best, a.y On Thu, 18 Aug 2016, Elijah Mak wrote: Thanks for the tips on reinitialisation of tracts. Apologies if I might have missed it in the online tutorial, do you have some general guidelines for reinitialising? Can I simply add "set reinit =1" to my configuration file, and then re-run trac-all -path. Are there any other parameters I could tweak? After running through more QC on other subjects, I have also noticed other tracts that were not fully constructed. These tracts appear to be truncated or blob-like, for a lack of better word :) I have attached the screenshot to illustrate what I mean. In these cases, I do the following QC routine after the general recon-all QC 1) freeview -v dmri/dtifit_FA.nii.gz -v dlabel/diff/aparc+aseg.bbr.nii.gz 2) freeview -v $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz subjectname/dmri/cvs/dtifit_FA.bbr.nii.gz Thanks a lot for your help, Anatasia! Best Wishes, Elijah -- Elijah Mak PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
Hi Elijah - It looks like the CVS case needs to be reinitialized. In principle you're right that if the registration is good this shouldn't be a problem. It's hard to tell what might've caused this in an individual case without looking at the data. If you want me to look into it you can upload all the TRACULA directories of the subject for me here: https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks! a.y On Thu, 18 Aug 2016, Elijah Mak wrote: Dear Anastasia and List, I have been using TRACULA to process my DTI dataset using both the affine MNI and non-linear CVS options. In one subject, the forceps major (MNI) look very different from its CVS counterpart (screenshot attached). I am just wondering what could lead to this type of differences? I've checked the registrations and they look good (overlaying FA on MNI/CVS). Thanks! Best Wishes, Elijah -- Elijah Mak PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] opening at the University of Sydney
-- Forwarded message -- Date: Tue, 16 Aug 2016 22:55:47 + From: Sasha Klistorner Research Fellow - Neuroimaging Save Sight Institute and Brain and Mind Centre Sydney Medical School Reference no. 1332/0816 · Join a collaborative and supportive research team · Bring your expertise in neuroimaging to this important research in multiple sclerosis · Full-time fixed term for one year, remuneration package: base salary $99K-$117K p.a., leave loading and up to 17% superannuation The University of Sydney is Australia's first university and has an outstanding global reputation for academic and research excellence. It employs over 7600 permanent staff, supporting over 60,000 students. Save Sight Institute leads research into eye diseases and conditions, throughout Australia and internationally. Our renowned team of laboratory and clinical researchers are at the forefront of ophthalmic breakthroughs, and our findings have already saved the sight of many people living with eye disease since the institute was formed in 1985. The Brain and Mind Centre’s multidisciplinary research aims to set new standards in brain and mind sciences both in Australia and internationally, is dedicated to finding solutions that will lead to generational change. Our approach is based on the active collaboration of researchers from basic through to translational and clinical brain and mind sciences, students, patients and front-line carers. We are seeking to appoint a Research Fellow to work under the combined supervision of Associate Professor Alexander (Sasha) Klistorner at the Save Sight Institute and Associate Professor Michael Barnett at the Brain and Mind Centre. These world-class researchers are interested in the development of neuroimaging biomarkers of demyelination and axonal loss and the study of the mechanisms of axonal degeneration in multiple sclerosis using the visual system as a model. You will have the opportunity to actively participate in research in this area. In this role you will: * work closely with clinical, scientific, imaging and other relevant university staff at the Save Sight Institute and the Brain and Mind Centre, and the Sydney Neuroimaging Analysis Centre to develop and/or refine magnetic resonance imaging protocols and analysis pipelines relevant to the project * be required to develop and implement a tool for the longitudinal analysis of diffusion tensor imaging (DTI) alterations in multiple sclerosis patients * provide expertise across aspects of magnetic resonance imaging acquisition, protocol design and writing, analysis and interpretation of data relevant to the project; and contribute to writing peer-reviewed manuscripts * take responsibility for the supervision of research assistants / image analysts working on the project or related projects where relevant · undertake administration relating to your own university activities. You may also have the opportunity to work on other related team projects and to supervise postgraduate research students or projects and be involved in research training. To succeed in securing this role you will have: · a PhD in neuroimaging or a related discipline · knowledge of MRI analytics, physics, mathematical and computational modelling · strong experience in MRI image processing and analysis · solid experience in basic neuroimaging toolboxes such as FSL, FreeSurfer or similar analytical packages · experience in Diffusion MR data analysis · demonstrated experience writing complex analytical reports and papers · ability to work both independently and as part of a multidisciplinary team · programming skills in bash-scripting, Matlab and/or Python · sound organisational skills and ability to effectively manage competing priorities___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA extracting diffusion measures using ASEG or WM parc
Hi Yoon - Please see "FA ROI analysis" in the diffusion tutorial on the freesurfer wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion_DtiIntegration#FAROIAnalysis Best, a.y On Mon, 15 Aug 2016, Chung, Yoonho wrote: Hi Anastasia, Is it possible to extract diffusion measures FA, ADC etc. within the subcortical (ASEG) or WM parc ROI regions using the Freesurfer tools? If possible, can you show how it can be done? Thank you in advance. Best, Yoon ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FreeSurfer TrackVis Transforms
Hi - Check out the dmri_trk2trk command. In your case, you'd need to pass it a transformation file from the registration between your diffusion and structural data, which you can compute with bbregister. Best, a.y On Mon, 15 Aug 2016, "김재명" wrote: Dear expert. Hi. I'm a newbie using Freesurfer software, and I want to transform the data of .trk file which is from Trackvis tool. (https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms) As there is an information for transforming trk file into the space of Freesurfer surface, I read it several times but I couldn't implement it on Linux console. The problem is that I cannot understand how to 'load the trk data from a file' to use the header data such as voxel_size. I also read TrackVis file format (at http://trackvis.org/docs/?subsect=fileformat), and read other mails sent from others, but couldn't solve the problem. Could you give me a specific steps to solve this? Many thanks Jack. [IMAGE] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] How to run part of TRACULA
Hi Nasia - They both have preprocessing steps because recon-all runs on the T1 and trac-all runs on the DWIs, so they preprocess different images. You cannot skip any of the steps in recon-all and still get a segmentation. The point of the autorecon schemes is mostly to repeat only one part of the processing if you change something in between, not to skip part of the processing entirely. Best, a.y On Sun, 14 Aug 2016, Athanasia Metoki wrote: Dear Anastasia, Thank you so much for responding so fast! I see what you're saying and thank you for your input. I have one more question if you don't mind taking a moment to respond. I noticed that both trac-all and recon-all include some preprocessing steps (eg. motion correction, eddy current correction, skull stripping). How come and they both have these steps if one is supposed to run both commands? My understandind is, if someone wants to run TRACULA from scratch, they would need to run both recon-all (first) and trac-all (second). One would have to run recon-all in order to get the cortical parcellation and subcortical segmentation (mri/aparc+aseg.mgz) file which will be used from trac-all in the mask creation step. In my case where I have some preprocessed data, is there a particular -autorecon# command which only does some of the recon steps that would help me get the cortical parcellation and subcortical segmentation (mri/aparc+aseg.mgz) file that I am missing? I understand I may be asking a lot! Once more thank you very much for your initial response and your time! Best, Nasia Metoki On Sat, Aug 13, 2016 at 8:03 PM, Anastasia Yendiki wrote: Hi Athanasia - TRACULA expects certains files named a certain way to be there at the end of each preprocessing step. These are described here: https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfile s If you are using pre-existing files, you have to make sure that they follow the same file/directory naming convention. You just run recon-all with the default settings. The aparc+aseg is created in one of the last steps of recon-all, so all the previous steps have to run as well. Hope this helps! a.y On Sat, 13 Aug 2016, Athanasia Metoki wrote: > Dear Freesurfer Developers, > > I am fairly new to image analysis and this is the first time I use > Freesurfer. > > I have some DTI data and I have already preprocessed them and ran bedpostX > using FSL. I ran probabilistic tractography on FSL as well to get the > connectivity between two distinct brain areas. > > I am also interested in getting the probability distribution for the > uncinate fasciculi so I am trying to use TRACULA. > My question is: Can I use TRCULA without doing preprocessing and dedpostX > again? If so, will I need to do the cortical parcelation and subcortical > segmentation with recon-all and get the aparc+aseg.mgz file in order to use > TRACULA? Which argument would I need to use when I run recon-all? > > Thank you! > > Athanasia Metoki > Psychology Doctoral Student - Brain and Cognitive Sciences Program > Cognitive Neuroscience Laboratory > Temple University > Department of Psychology > 1701 N 13th St. > Philadelphia, PA 19122 > Email: athanasia.met...@temple.edu > >___ > > The contents of this email message and any attachments are intended solely > for the addressee(s) and may contain confidential and/or privileged > information and may be legally protected from disclosure. If you are not the > intended recipient of this message or their agent, or if this message has > been addressed to you in error, please immediately alert the sender by reply > email and then delete this message and any attachments. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > copying, or storage of this message or its attachments is strictly > prohibited. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-ma
Re: [Freesurfer] How to run part of TRACULA
Hi Athanasia - TRACULA expects certains files named a certain way to be there at the end of each preprocessing step. These are described here: https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputdirectoriesandfiles If you are using pre-existing files, you have to make sure that they follow the same file/directory naming convention. You just run recon-all with the default settings. The aparc+aseg is created in one of the last steps of recon-all, so all the previous steps have to run as well. Hope this helps! a.y On Sat, 13 Aug 2016, Athanasia Metoki wrote: > Dear Freesurfer Developers, > > I am fairly new to image analysis and this is the first time I use > Freesurfer. > > I have some DTI data and I have already preprocessed them and ran bedpostX > using FSL. I ran probabilistic tractography on FSL as well to get the > connectivity between two distinct brain areas. > > I am also interested in getting the probability distribution for the > uncinate fasciculi so I am trying to use TRACULA. > My question is: Can I use TRCULA without doing preprocessing and dedpostX > again? If so, will I need to do the cortical parcelation and subcortical > segmentation with recon-all and get the aparc+aseg.mgz file in order to use > TRACULA? Which argument would I need to use when I run recon-all? > > Thank you! > > Athanasia Metoki > Psychology Doctoral Student - Brain and Cognitive Sciences Program > Cognitive Neuroscience Laboratory > Temple University > Department of Psychology > 1701 N 13th St. > Philadelphia, PA 19122 > Email: athanasia.met...@temple.edu > > ___ > > The contents of this email message and any attachments are intended solely > for the addressee(s) and may contain confidential and/or privileged > information and may be legally protected from disclosure. If you are not the > intended recipient of this message or their agent, or if this message has > been addressed to you in error, please immediately alert the sender by reply > email and then delete this message and any attachments. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > copying, or storage of this message or its attachments is strictly > prohibited. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FW: TRACULA re-init error
Hi - Does this directory exist? ERROR: fio_pushd: /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni I'd have to see the entire trac-all.log file to tell you for sure. The first error may show up earlier than the one that causes the crash. Thanks, a.y On Mon, 8 Aug 2016, Song, Daniel wrote: > > > Dan > > _ > From: Ostrowski, Lauren > Sent: Monday, August 08, 2016 4:08 PM > To: Song, Daniel > Subject: FW: TRACULA re-init error > > > _ > From: Ostrowski, Lauren > Sent: Monday, August 08, 2016 4:04 PM > To: Freesurfer@nmr.mgh.harvard.edu > Subject: TRACULA re-init error > > Hi all, > > I'm running into a problem with TRACULA, when I try to re-initialize tracts > that failed to reconstruct during the first > run. I have set reinit = 1 in the configuration file and specified the > particular tracts that I want to reconstruct, but > when I try to run the "trac-all -prior" step, I keep getting this error > message: > > INFO: SUBJECTS_DIR is /autofs/cluster/neuromind/cat/bects/subjects > INFO: Diffusion root is /cluster/neuromind/cat/bects/subjects/pBECTS001/trac > Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/dev > trac-preproc -c > /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/dmrirc.local > -log /cluster/neuromi > nd/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/trac-all.log -cmd > /cluster/neuromind/cat/bects/subjects/pBECTS001/ > trac/pBECTS001/scripts/trac-all.cmd > #- > /usr/local/freesurfer/dev/bin/trac-preproc > #- > #@# Priors Mon Aug 8 15:53:46 EDT 2016 > /usr/local/freesurfer/dev/bin/dmri_train --outdir > /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/m > ni --out fmajor_PP_avg33_mni_bbr --slist /tmp/subj33.pBECTS001.15581.txt > --trk dlabel/mni/fmajor_PP.bbr.trk --seg dlabel/ > mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 --rois > dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/m > ni/fmajor_PP_roi2.bbr.nii.gz --bmask > /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lowb_brain > _mask.bbr.nii.gz --fa > /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz > --cptdir /clus > ter/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg > /cluster/neuromind/cat/bects/subjects/pBECTS0 > 01/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc > ERROR: fio_pushd: > /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni > cwd /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/dlabel/mni > cmdline /usr/local/freesurfer/dev/bin/dmri_train --outdir > /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/ > dlabel/mni --out fmajor_PP_avg33_mni_bbr --slist > /tmp/subj33.pBECTS001.15581.txt --trk dlabel/mni/fmajor_PP.bbr.trk --seg > dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 > --rois dlabel/mni/fmajor_PP_roi1.bbr.nii.gz > dlabel/mni/fmajor_PP_roi2.bbr.nii.gz --bmask > /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lo > wb_brain_mask.bbr.nii.gz --fa > /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz > --cptd > ir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff > --reg /cluster/neuromind/cat/bects/subjects > /pBECTS001/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc > sysname Linux > hostname truffles > machine x86_64 > user lo941 > Output directory: > /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni > Output directory in test subject's space: > /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/di > ff > Output base: fmajor_PP_avg33_mni_bbr > Training subject directory list: /tmp/subj33.pBECTS001.15581.txt > Location of streamline files relative to base: dlabel/mni/fmajor_PP.bbr.trk > Location of start ROI files relative to base: > dlabel/mni/fmajor_PP_roi1.bbr.nii.gz > Location of end ROI files relative to base: > dlabel/mni/fmajor_PP_roi2.bbr.nii.gz > Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz > Label ID's from aparc+aseg to add to cortex mask: 0 > Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz > Brain mask for output subject: Segmentation fault (core dumped) > Linux truffles 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 > x86_64 x86_64 x86_64 GNU/Linux > trac-preproc exited with ERRORS at Mon Aug 8 15:53:46 EDT 2016 > > Any help would be very much appreciated. It seems to me that TRACULA can't > find the aparc+aseg labels, but when I looked > at th
Re: [Freesurfer] TRACULA tract endpoints on cortical surface
Hi Barbara - This can be done with mri_vol2surf. The projection that's described in that passage can be done with --projdist-max -6 6 1, and the surface smoothing with --surf-fwhm 6. There are other options in mri_vol2surf, I'd recommend playing with the settings to see what works better for your data. Best, a.y On Fri, 5 Aug 2016, Barbara Kreilkamp wrote: > > Dear Freesurfers and TRACULA experts, > > Thank you for your help so far. I am trying to map the endpoints of the > tract probability distributions onto the cortical surface (as mentioned > in Solsnes et al. 2016 NI and Storsve et al. 2016 PLos). > > I've somehow gathered that I need to do this (example one endpoint): > > flirt -ref /mri/orig/T1.nii.gz -in > dpath/rh.ilf_AS_avg33_mni_bbr/endpt2.pd.nii.gz -applyxfm -init > /dmri/xfms/diff2anat.bbr.mat > > I then loaded the images in Freeview and they look reasonable together > with the lh.white and lh.pial surfaces: freeview -v /mri/brain -tv > dapth/rh.ilf_AS_agv33_mni_bbr/endpt2_anat.pd.nii.gz > > What I don't get is how to do this: > > "we projected the tract endpoints onto the gray/white matter surface by > sampling along the surface normal vector, anywhere within 6 mm (3 > DWI-space voxels) of the gray/white junction and then smoothing along > the surface with a 2D Gaussian kernel of 6mm full width at half max." > (Solsnes et al. 2016) > > Any help would be greatly appreciated. > > Best wishes, > Barbara > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coordinates in TRACULA group analysis
That's correct! On Wed, 3 Aug 2016, Anri WATANABE wrote: Hi Anastasia, Thank you for your kind explanation. I can be understanding how TRACULA tracts white matter pathways. At each position (in training subjects, not in new subjects of my data) probability that next goes for which direction to every labels in the aparc+aseg (not with setting a certain ROI) is computed with use of training subjects. The prior probabilities are made from training subjects (your publication in 2011) and they are based on manual labeling (the manual labeling tracts are referred to Wakana et al. 2007). Then when white matter pathways are reconstructed in my subjects, TRACULA computes anatomical priors in each subjects in my data in pre-processing and probability distributions from anatomical priors and by fitting ball-and-stick model. Is this comprehension ok? Best Regards, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki : Hi Anri - Instead of hard-coding some ROIs in the white matter that the tract is forced to go through, TRACULA uses information like "what is the probability that this tract goes lateral/anterior/etc to XXX", where XXX any of the labels in the aparc+aseg. TRACULA computes these prior probabilities from a set of training subjects, where the tracts have been labeled manually. So it knows how likely a tract is to go through a certain aparc+aseg label, or to he left, right, anterior, etc of a certain aparc+aseg label. This is computed separately at each position along the tract. It's computed from the training subjects, and then used when reconstructing the tract in the new subject that you run TRACULA on. Hope this helps, a.y On Sun, 31 Jul 2016, Anri WATANABE wrote: Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if ROIs are not set how determine the origin and the end of a certain tract? I think that the first we have to determine the origin and the end of the tract, the second it constructs possible pathway not with the deterministic way (only 1 direction / 1 voxel) but with the probabilistic way (considering which direction should be next to). Is this comprehension wrong? Thank you. Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki : Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic model of how likely each tract is to go through or next to each of the labels of the freesurfer subcortical segmentation and cortical parcellation, as a function of position along the trajectory of the tract. Best, a.y On Sun, 31 Jul 2016, Anri WATANABE wrote: Hi Anastasia, Thank you! It seems work well!! I have another question. Are ROIs for automatic tractography in TRACULA the same ROIs presented in Wakana et al. 2007? Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki : Hi Anri - The problem is in this line: set cmd = ($cmd --ref $cvstempdir/$cvstemp) It shoul
Re: [Freesurfer] Coordinates in TRACULA group analysis
Hi Anri - Instead of hard-coding some ROIs in the white matter that the tract is forced to go through, TRACULA uses information like "what is the probability that this tract goes lateral/anterior/etc to XXX", where XXX any of the labels in the aparc+aseg. TRACULA computes these prior probabilities from a set of training subjects, where the tracts have been labeled manually. So it knows how likely a tract is to go through a certain aparc+aseg label, or to he left, right, anterior, etc of a certain aparc+aseg label. This is computed separately at each position along the tract. It's computed from the training subjects, and then used when reconstructing the tract in the new subject that you run TRACULA on. Hope this helps, a.y On Sun, 31 Jul 2016, Anri WATANABE wrote: Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if ROIs are not set how determine the origin and the end of a certain tract? I think that the first we have to determine the origin and the end of the tract, the second it constructs possible pathway not with the deterministic way (only 1 direction / 1 voxel) but with the probabilistic way (considering which direction should be next to). Is this comprehension wrong? Thank you. Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki : Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic model of how likely each tract is to go through or next to each of the labels of the freesurfer subcortical segmentation and cortical parcellation, as a function of position along the trajectory of the tract. Best, a.y On Sun, 31 Jul 2016, Anri WATANABE wrote: Hi Anastasia, Thank you! It seems work well!! I have another question. Are ROIs for automatic tractography in TRACULA the same ROIs presented in Wakana et al. 2007? Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki : Hi Anri - The problem is in this line: set cmd = ($cmd --ref $cvstempdir/$cvstemp) It should be changed to this: set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz) For this to take effect, you need to run "which trac-all" and make the change in the trac-all file that the which commands shows you. Hope this helps, a.y On Fri, 15 Jul 2016, Anri WATANABE wrote: Hi, AnastasiaThis is trac-all.local-copy from 1 subject. Thank you! Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki : Hi Anri - This may be a bug that was fixed at some point. Can you send me the scripts/trac-all.local-copy from one of your subjects? Thanks! a.y On Mon, 11 Jul 2016, Anri WATANABE wrote: Hi Anastasia,There is an error in .log files of left corticospinal tract in cvs template and I attached one of file. In addition .log files of right c
Re: [Freesurfer] Coordinates in TRACULA group analysis
Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic model of how likely each tract is to go through or next to each of the labels of the freesurfer subcortical segmentation and cortical parcellation, as a function of position along the trajectory of the tract. Best, a.y On Sun, 31 Jul 2016, Anri WATANABE wrote: Hi Anastasia, Thank you! It seems work well!! I have another question. Are ROIs for automatic tractography in TRACULA the same ROIs presented in Wakana et al. 2007? Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki : Hi Anri - The problem is in this line: set cmd = ($cmd --ref $cvstempdir/$cvstemp) It should be changed to this: set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz) For this to take effect, you need to run "which trac-all" and make the change in the trac-all file that the which commands shows you. Hope this helps, a.y On Fri, 15 Jul 2016, Anri WATANABE wrote: Hi, AnastasiaThis is trac-all.local-copy from 1 subject. Thank you! Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki : Hi Anri - This may be a bug that was fixed at some point. Can you send me the scripts/trac-all.local-copy from one of your subjects? Thanks! a.y On Mon, 11 Jul 2016, Anri WATANABE wrote: Hi Anastasia,There is an error in .log files of left corticospinal tract in cvs template and I attached one of file. In addition .log files of right corticospinal tract in cvs template doesn't exist. Thanks in advance. Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki : Hi Anri - Is there an error in the stats/*.log files for the different tracts? a.y On Tue, 5 Jul 2016, Anri WATANABE wrote: Dear Anastasia, I use TRACULA to obtain diffusion measures at each voxel in a certain pathway for group analysis, but there aren't stats/*.path.mean.txt files. I found .log files (_PP.avg33_mni_bbr.log) which exist 1 file per 1 tract, except corticospinal tract which has 2 .log files. Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example Error log: Loading output reference volume from /Applications/freesurfer/subjects/cvs_avg35 corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35 I attached dmrirc.example (configuration
Re: [Freesurfer] TRACULA: 20% default threshold
Yes, same thing! On Wed, 27 Jul 2016, Harms, Michael wrote: Thanks for clarifying. Is the same true for the --pthr option of dmri_pathstats as well? i.e., --pthr is specifying the portion of the 99th percentile, not the strict maximum? thx, -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 7/26/16, 11:40 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Dillan - Thank you for your support! Because the maximum value can sometimes be an outlier, we use the values of the 99th percentile instead. In the absence of an outlier this would be very close to the maximum. Best, a.y On Tue, 26 Jul 2016, Newbold, Dillan wrote: Hi everyone, I’m having a little trouble understanding the exact meaning of the 20% default threshold used in the freeview -tv option and dmri_pathstats --pthr. I’ve seen multiple threads where Anastasia said that it is 20% of the maximum value in the probability distribution—which corresponds to the maximum number of sample paths intersecting a single voxel—but the default thresholds I’ve seen set by the -tv option are generally lower than that. For example, I have one subject in whom the right CST has a maximum value in its path.pd.nii.gz file of 300. I would expect based on what I’ve read in the mail archives that the threshold would be set at 60, but when I open the merged file with the -tv option the default threshold for the right CST is 35. My current best guess is that the default threshold is set to produce a volume that has a probability sum equal to 20% of the sum of the pre-threshold volume. (That is, the sum of intensities of all voxels in the path.pd.nii.gz file should be 5 times the sum of the voxels above the default threshold.) Is that accurate? Thanks for all you’ve done to develop this tool. It’s brilliant and I want to understand as much of it as I can. -Dillan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA fornix tractography
Hopefully soon, as several people have asked for it, but I don't have a concrete date unfortunately. On Wed, 27 Jul 2016, Barbara Kreilkamp wrote: > Dear Anastasia, > > Thank you that is great! Do you know yet when it will be available? > > Best wishes, > > Barbara > > > On 27/07/2016 06:25, Anastasia Yendiki wrote: >> Hi Barbara - We're working on a new atlas for TRACULA that will include >> the fornix. We've already done the manual labeling for it. >> >> Best, >> >> a.y >> >> On Mon, 25 Jul 2016, Barbara Kreilkamp wrote: >> >>> Dear Anastasia, >>> >>> As we are analyzing DTI data acquired in patients with epilepsy we are >>> especially interested in the fornix. >>> I've come across the mri_cc -f option for fornix segmentation (native space) >>> but I've also read that manual tracing/labeling of the tracts would be >>> needed in the 33 controls for TRACULA (training set - trctrain). >>> In Wakana et al. 2011 I see that the fornix was not included due to low >>> reproducibility and it further states: >>> >>> "the reason for the poor reproducibility is most likely due to not enough >>> spatial resolution with respect to the diameter" >>> >>> I wonder if you could please guide us in how to best add this tract to >>> TRACULA so that it would be consistent in the methods compared with the >>> other tract ROI definitions or perhaps state what were the difficulties in >>> adding this particular tract to TRACULA. >>> >>> Thank you very much, >>> Best wishes, >>> Barbara >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA: 20% default threshold
Hi Dillan - Thank you for your support! Because the maximum value can sometimes be an outlier, we use the values of the 99th percentile instead. In the absence of an outlier this would be very close to the maximum. Best, a.y On Tue, 26 Jul 2016, Newbold, Dillan wrote: Hi everyone, I’m having a little trouble understanding the exact meaning of the 20% default threshold used in the freeview -tv option and dmri_pathstats --pthr. I’ve seen multiple threads where Anastasia said that it is 20% of the maximum value in the probability distribution—which corresponds to the maximum number of sample paths intersecting a single voxel—but the default thresholds I’ve seen set by the -tv option are generally lower than that. For example, I have one subject in whom the right CST has a maximum value in its path.pd.nii.gz file of 300. I would expect based on what I’ve read in the mail archives that the threshold would be set at 60, but when I open the merged file with the -tv option the default threshold for the right CST is 35. My current best guess is that the default threshold is set to produce a volume that has a probability sum equal to 20% of the sum of the pre-threshold volume. (That is, the sum of intensities of all voxels in the path.pd.nii.gz file should be 5 times the sum of the voxels above the default threshold.) Is that accurate? Thanks for all you’ve done to develop this tool. It’s brilliant and I want to understand as much of it as I can. -Dillan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] flipping TRACULA tracts
Hi Barbara - Your hack sounds like the right idea. One option would be to switch the FA values between the pathstats.byvoxel.txt files in the lh.* and rh.* output directories, by editing the text files without renaming the directories. Hope this helps, a.y On Mon, 25 Jul 2016, Barbara Kreilkamp wrote: > Dear Freesurfers, > > I've got data pertaining to patients with left and right-sided temporal > lobe epilepsy (TLE). > My aim is to group those tracts according to side of epilepsy for > waypoint comparisons. > > Basically for patients with right TLE I'd like to look at right tracts > and at the same time for patients with left TLE I'd like to look at left > tracts (ipsilateral tracts), I need to do the same for the contralateral > tracts. > Is there a straightforward way of doing this? > > I've already copied the tracts to respective ipsi and contralateral > byvoxel.txt files. Like so: for i in R*/dpath/rh*/pathstats.byvoxel.txt; > do cp $i ${i/byvoxel./byvoxel_ipsiRTLE.}; done ; for i in > R*/dpath/lh*/pathstats.byvoxel.txt; do cp $i > ${i/byvoxel./byvoxel_contraRTLE.}; done > Now I have to flip the x-coordinates in the patients with right TLE (to > make them more comparable to the tracts of the patients with left TLE). > That will not be a problem, but I wonder if I am missing something? > Can I then just go ahead and run trac-all -stats -c dmrircfile to > generate the mean waypoint tracts etc.? > > Thank you very much, > Best wishes, > > Barbara > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA fornix tractography
Hi Barbara - We're working on a new atlas for TRACULA that will include the fornix. We've already done the manual labeling for it. Best, a.y On Mon, 25 Jul 2016, Barbara Kreilkamp wrote: > Dear Anastasia, > > As we are analyzing DTI data acquired in patients with epilepsy we are > especially interested in the fornix. > I've come across the mri_cc -f option for fornix segmentation (native space) > but I've also read that manual tracing/labeling of the tracts would be > needed in the 33 controls for TRACULA (training set - trctrain). > In Wakana et al. 2011 I see that the fornix was not included due to low > reproducibility and it further states: > > "the reason for the poor reproducibility is most likely due to not enough > spatial resolution with respect to the diameter" > > I wonder if you could please guide us in how to best add this tract to > TRACULA so that it would be consistent in the methods compared with the > other tract ROI definitions or perhaps state what were the difficulties in > adding this particular tract to TRACULA. > > Thank you very much, > Best wishes, > Barbara > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA dmri_paths, single time point in longitudinal stream
Hi Michael - Which build of freesurfer do you use? I can send you the new version of dmri_paths so you can try it out. Best, a.y On Wed, 20 Jul 2016, Harms, Michael wrote: Hi Anastasia, I was wondering what the resolution to this thread was: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg42734.html It sounds like a new version of dmri_paths was deemed necessary to appropriately process single time points in the longitudinal TRACULA stream, but Janosch’s last post seemed to indicate that her issue wasn’t resolved even with the new build of dmri_paths that you generated. thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA group stats visualization
Hi Derek - Good to know things worked out! a.y On Tue, 19 Jul 2016, Derek Pisner wrote: > Hi Anastasia, > > I thought I should let you know that this issue has now been resolved. We > specified the base ID's/ subject ID's incorrectly in the config file! Sorry > for the confusion. Now our group output looks correct. > > Thanks for your help, > Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Derek Pisner > [dpis...@psychiatry.arizona.edu] > Sent: Tuesday, July 12, 2016 5:06 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Anastasia, > > All subjects had both time-points (for DWI and T1-weighted recons). The > recons were run following the standard longitudinal pipeline for FS. > > Would it matter that I ran the pipeline piecemeal (i.e. separate > configuration files for each subject--see attached example)? In case you are > wondering, I did it this way in order to run the pipeline in parallel (i.e. > by subject) on our cluster... > > Another consideration is that we did preprocessing outside of TRACULA (i.e. > using FSL's tools directly so that we could apply a fieldmap, use new EDDY > with TOPUP, as well as apply a denoising algorithm). We then setup the folder > structure and filenames to begin TRACULA at the trac-all -intra stage, which > we have done successfully in the past when not using the longitudinal > pipeline (i.e. single-subject analyses) > > Still, I have a feeling that none of these customizations should have made > any difference as our merged outputs look excellent for both timepoints, for > all subjects... Any other thoughts about what might be causing this? > > Kind regards, > -Derek > ________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Tuesday, July 12, 2016 1:45 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't > been able to replicate the problem in our own longitudinal data. Did you > by any chance have any subjects that had only a single time point? > > a.y > > On Thu, 7 Jul 2016, Derek Pisner wrote: > >> Sure thing. fmajor mean.txt file is attached. >> >> >> Thanks a bunch, >> -Derek >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Thursday, July 07, 2016 4:48 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA group stats visualization >> >> Hi Derek - this is strange. The dev and 5.3 version of freeview should >> display them differently. Can you send me one of those mean.txt files? >> >> a.y >> >> On Wed, 6 Jul 2016, Derek Pisner wrote: >> >>> Hi Anastasia, >>> >>> This occurs for me on both stable and dev versions of freview and trac-all >>> -stat >>> >>> -Derek >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >>> [ayend...@nmr.mgh.harvard.edu] >>> Sent: Monday, July 04, 2016 12:47 AM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] TRACULA group stats visualization >>> >>> Hi Derek - Are you by any chance using the dev version of freeview? >>> >>> a.y >>> >>> On Fri, 1 Jul 2016, Derek Pisner wrote: >>> >>>> Dear Anastasia, >>>> I am running into an issue with the trac-all -stat option on our >>>> longitudinal TRACULA data. >>>> >>>> Everything runs smoothly through all earlier stages, and I checked >>>> individual subjects' merged outputs in freeview with -tv mode. Everything >>>> looks fine. >>>> >>>> Also, then when I run trac-all -c dmric_config -stat, everything finishes >>>> without error. >>>> >>>> But then when I open the results with the command: >>>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >>>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >>>> >>>> I get the image seen in the attached .png
Re: [Freesurfer] Coordinates in TRACULA group analysis
Hi Anri - The problem is in this line: set cmd = ($cmd --ref $cvstempdir/$cvstemp) It should be changed to this: set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz) For this to take effect, you need to run "which trac-all" and make the change in the trac-all file that the which commands shows you. Hope this helps, a.y On Fri, 15 Jul 2016, Anri WATANABE wrote: Hi, AnastasiaThis is trac-all.local-copy from 1 subject. Thank you! Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki : Hi Anri - This may be a bug that was fixed at some point. Can you send me the scripts/trac-all.local-copy from one of your subjects? Thanks! a.y On Mon, 11 Jul 2016, Anri WATANABE wrote: Hi Anastasia,There is an error in .log files of left corticospinal tract in cvs template and I attached one of file. In addition .log files of right corticospinal tract in cvs template doesn't exist. Thanks in advance. Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki : Hi Anri - Is there an error in the stats/*.log files for the different tracts? a.y On Tue, 5 Jul 2016, Anri WATANABE wrote: Dear Anastasia, I use TRACULA to obtain diffusion measures at each voxel in a certain pathway for group analysis, but there aren't stats/*.path.mean.txt files. I found .log files (_PP.avg33_mni_bbr.log) which exist 1 file per 1 tract, except corticospinal tract which has 2 .log files. Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example Error log: Loading output reference volume from /Applications/freesurfer/subjects/cvs_avg35 corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35 I attached dmrirc.example (configuration file) and /scripts/trac-all.log. Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-06-03 9:51 GMT+09:00 Anri WATANABE : Hi, Anastasia. There aren't any .log files but text files like lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text files complete all pathways and measures. ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-06-02 3:03 GMT+09:00
Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message
Hi Knut Jørgen - Do you get this error only with the dev version of freesurfer? The command line causing the error is: bbregister --s 4_test --init-fsl --dti --mov /home/knutjbj/subjects/4_test/dmri/dwi.nii.gz --reg /home/knutjbj/subjects/4_test/dmri/xfms/anatorig2diff.bbr.dat --fslmat /home/knutjbj/subjects/4_test/dmri/xfms/diff2anatorig.bbr.mat Can you please try running this with the 5.3 version? Thanks! a.y On Wed, 13 Jul 2016, Knut J Bjuland wrote: Hi Anastasia Thanks. I am sending my entire trac-all.log Knut Jøgen On 07/12/2016 11:19 PM, Anastasia Yendiki wrote: Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks! a.y On Mon, 11 Jul 2016, Knut J Bjuland wrote: flirt.fsl -ref /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/ref vol.fslregister.nii -in /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/mov vol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fs l.mat -init /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fsl mat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt Fedora 24 glibc-2.23.1-8.fc24.x86_64 gcc-6.1.1-3.fc24.x86_64 libstdc++-6.1.1-3.fc24.x86_64 ldd /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x7ffe8b6c8000) libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x7feaeb67e000) libm.so.6 => /lib64/libm.so.6 (0x7feaeb374000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7feaeb15d000) libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000) /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000) Knut Jørgen Bjuland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] When I am run trac-all in Fedora 24 with the developmental version of FreeSurfer, it crashes when running flirt.fsl with this error message
Hi Knut Jørgen - Can you please send your entire trac-all.log? Thanks! a.y On Mon, 11 Jul 2016, Knut J Bjuland wrote: flirt.fsl -ref /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/refvol.fslregister.nii -in /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/reg.init.dat.fsl.mat -init /home/knutjbj/subjects/023v4/dmri/xfms/tmp.bbregister.35024/fslregister/fslmat0.trans.mat -schedule /usr/local/freesurfer/bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt Fedora 24 glibc-2.23.1-8.fc24.x86_64 gcc-6.1.1-3.fc24.x86_64 libstdc++-6.1.1-3.fc24.x86_64 ldd /usr/local/freesurfer/bin/flirt.fsl linux-vdso.so.1 (0x7ffe8b6c8000) libz.so.1 => /lib64/libz.so.1 (0x7feaeba06000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x7feaeb67e000) libm.so.6 => /lib64/libm.so.6 (0x7feaeb374000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x7feaeb15d000) libc.so.6 => /lib64/libc.so.6 (0x7feaead9a000) /lib64/ld-linux-x86-64.so.2 (0x557ba6f46000) Knut Jørgen Bjuland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coordinates in TRACULA group analysis
Hi Anri - This may be a bug that was fixed at some point. Can you send me the scripts/trac-all.local-copy from one of your subjects? Thanks! a.y On Mon, 11 Jul 2016, Anri WATANABE wrote: Hi Anastasia,There is an error in .log files of left corticospinal tract in cvs template and I attached one of file. In addition .log files of right corticospinal tract in cvs template doesn't exist. Thanks in advance. Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki : Hi Anri - Is there an error in the stats/*.log files for the different tracts? a.y On Tue, 5 Jul 2016, Anri WATANABE wrote: Dear Anastasia, I use TRACULA to obtain diffusion measures at each voxel in a certain pathway for group analysis, but there aren't stats/*.path.mean.txt files. I found .log files (_PP.avg33_mni_bbr.log) which exist 1 file per 1 tract, except corticospinal tract which has 2 .log files. Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example Error log: Loading output reference volume from /Applications/freesurfer/subjects/cvs_avg35 corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35 I attached dmrirc.example (configuration file) and /scripts/trac-all.log. Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-06-03 9:51 GMT+09:00 Anri WATANABE : Hi, Anastasia. There aren't any .log files but text files like lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text files complete all pathways and measures. ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-06-02 3:03 GMT+09:00 Anastasia Yendiki : Thanks, Anri. So the previous steps seem to have run fine. Are there any .log files created in the stats/ folder, which is created by trac-all -stat? On Wed, 1 Jun 2016, Anri WATANABE wrote: Hi Anastasia, This is a /scripts/trac-all.log of one subject of the group. Thanks, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-05-31 22:55 GMT+09:00 Anastasia Yendiki : Hi Anri - Can you also send your log file (scripts/trac-all.log)? I'll need to see what exactly was running when the error occurred. Thanks! a.y On Sat, 28 May 2016, Anri WATANABE wrote: Hello Anastasia,sorry for few information and let me tell you command and error log. Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example Error log: Loading outp
Re: [Freesurfer] TRACULA tract group comparison p-values
Hi Barbara - Unfortunately we are very limited right now in our options for point set overlay display. I guess there's nothing that would be more suitable for displaying values that go all the way from negative to positive (which is what I suspect you have). I'll submit this request to freeview headquarters :) Hopefully we can get it in there quickly. Thanks for your patience! a.y On Sun, 10 Jul 2016, Barbara Kreilkamp wrote: > Dear Anastasia, > > Thank you, yes that was exactly what I was attempting to do. Would you > be able to assist me with this following question as well please? > > How would I be able to use a different colormap under point sets please? > I can only find "solid color" and "heatmap" but for example a > blue-yellow-to-red colormap would suit my needs more. > > Thank you, > > Best wishes, > > Barbara > > > On 07/07/2016 13:52, Anastasia Yendiki wrote: >> Hi Barbara - I don't believe that freeview has an option to show colorbars >> for heat maps that are loaded onto waypoints (if that's what you're >> trying to display). We should definitely add it in the future. >> >> Best, >> a.y >> >> On Wed, 6 Jul 2016, Barbara Kreilkamp wrote: >> >>> Dear Freesurfers, >>> >>> I am looking for a way to add a colorbar to my p-value tract cores >>> generated through TRACULA. >>> >>> When I load up the images as described in the tutorial here >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics >>> >>> I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and >>> there is no option to select my textfile with the p-values unfortunately. >>> >>> Would you please help? >>> >>> Thanks ever so, >>> >>> Barbara >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Fwd: TRACULA stat extraction issue
Hi Shashwath - Unfortunately this is not possible right now, so you'd have to add those extra columns after you run it. a.y On Fri, 8 Jul 2016, Shashwath Meda wrote: Hi Anastasia - Yes thats what i figured, however the way our pipeline system is setup this was the most straightfoward way of doing it. Anyways i did figure out how to extract the average values in a more convoluted fashion so we are all set with that. However, im trying to do the same with the trac-all -stat command now to extract pathbyvoxel stats and am having issues. I see that while assimilating group level info, the program automatically rejects or doesnt ouput a column for the subject that has failed, is there a quick and dirty fix to the code that will enable me to output all subjects data even if its failed (maybe replace the values with NaN or somethign similar for failed subjects?). Please let me know. Thanks Shashwath On Mon, Jul 4, 2016 at 3:25 AM, Anastasia Yendiki wrote: Hi Shashwath - It looks like you have modified the directory structure of the output files. Normally the dpath/ directory is right under the directory with subject's name. From your file of inputs, it looks like you've created some other subdirectories and now dpath/ is a few levels down the hierarchy. I'd recommend reverting to the original structure that the commands expect. Best, a.y On Fri, 10 Jun 2016, Shashwath Meda wrote: Dear Group - I seem to have run into an issue when attempting to assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts. The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation? tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table -- Best, Shashwath ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Best, Shashwath ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA group stats visualization
Hi Derek - Indeed this looks not to be in MNI coordinates, and I haven't been able to replicate the problem in our own longitudinal data. Did you by any chance have any subjects that had only a single time point? a.y On Thu, 7 Jul 2016, Derek Pisner wrote: > Sure thing. fmajor mean.txt file is attached. > > > Thanks a bunch, > -Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Thursday, July 07, 2016 4:48 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - this is strange. The dev and 5.3 version of freeview should > display them differently. Can you send me one of those mean.txt files? > > a.y > > On Wed, 6 Jul 2016, Derek Pisner wrote: > >> Hi Anastasia, >> >> This occurs for me on both stable and dev versions of freview and trac-all >> -stat >> >> -Derek >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Monday, July 04, 2016 12:47 AM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] TRACULA group stats visualization >> >> Hi Derek - Are you by any chance using the dev version of freeview? >> >> a.y >> >> On Fri, 1 Jul 2016, Derek Pisner wrote: >> >>> Dear Anastasia, >>> I am running into an issue with the trac-all -stat option on our >>> longitudinal TRACULA data. >>> >>> Everything runs smoothly through all earlier stages, and I checked >>> individual subjects' merged outputs in freeview with -tv mode. Everything >>> looks fine. >>> >>> Also, then when I run trac-all -c dmric_config -stat, everything finishes >>> without error. >>> >>> But then when I open the results with the command: >>> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >>> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >>> >>> I get the image seen in the attached .png file. Any idea what might be >>> causing this? >>> >>> Many thanks in advance for you help. >>> >>> Best, >>> Derek >>> >>> >>> >>> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] TRACULA tract group comparison p-values
Hi Barbara - I don't believe that freeview has an option to show colorbars for heat maps that are loaded onto waypoints (if that's what you're trying to display). We should definitely add it in the future. Best, a.y On Wed, 6 Jul 2016, Barbara Kreilkamp wrote: > Dear Freesurfers, > > I am looking for a way to add a colorbar to my p-value tract cores > generated through TRACULA. > > When I load up the images as described in the tutorial here > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics > > I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and > there is no option to select my textfile with the p-values unfortunately. > > Would you please help? > > Thanks ever so, > > Barbara > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA group stats visualization
Hi Derek - this is strange. The dev and 5.3 version of freeview should display them differently. Can you send me one of those mean.txt files? a.y On Wed, 6 Jul 2016, Derek Pisner wrote: > Hi Anastasia, > > This occurs for me on both stable and dev versions of freview and trac-all > -stat > > -Derek > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Monday, July 04, 2016 12:47 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] TRACULA group stats visualization > > Hi Derek - Are you by any chance using the dev version of freeview? > > a.y > > On Fri, 1 Jul 2016, Derek Pisner wrote: > >> Dear Anastasia, >> I am running into an issue with the trac-all -stat option on our >> longitudinal TRACULA data. >> >> Everything runs smoothly through all earlier stages, and I checked >> individual subjects' merged outputs in freeview with -tv mode. Everything >> looks fine. >> >> Also, then when I run trac-all -c dmric_config -stat, everything finishes >> without error. >> >> But then when I open the results with the command: >> freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w >> /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt >> >> I get the image seen in the attached .png file. Any idea what might be >> causing this? >> >> Many thanks in advance for you help. >> >> Best, >> Derek >> >> >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coordinates in TRACULA group analysis
Hi Anri - Is there an error in the stats/*.log files for the different tracts? a.y On Tue, 5 Jul 2016, Anri WATANABE wrote: Dear Anastasia, I use TRACULA to obtain diffusion measures at each voxel in a certain pathway for group analysis, but there aren't stats/*.path.mean.txt files. I found .log files (_PP.avg33_mni_bbr.log) which exist 1 file per 1 tract, except corticospinal tract which has 2 .log files. Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example Error log: Loading output reference volume from /Applications/freesurfer/subjects/cvs_avg35 corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35 I attached dmrirc.example (configuration file) and /scripts/trac-all.log. Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-06-03 9:51 GMT+09:00 Anri WATANABE : Hi, Anastasia. There aren't any .log files but text files like lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text files complete all pathways and measures. ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-06-02 3:03 GMT+09:00 Anastasia Yendiki : Thanks, Anri. So the previous steps seem to have run fine. Are there any .log files created in the stats/ folder, which is created by trac-all -stat? On Wed, 1 Jun 2016, Anri WATANABE wrote: Hi Anastasia, This is a /scripts/trac-all.log of one subject of the group. Thanks, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-05-31 22:55 GMT+09:00 Anastasia Yendiki : Hi Anri - Can you also send your log file (scripts/trac-all.log)? I'll need to see what exactly was running when the error occurred. Thanks! a.y On Sat, 28 May 2016, Anri WATANABE wrote: Hello Anastasia,sorry for few information and let me tell you command and error log. Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example Error log: Loading output reference volume from /Applications/freesurfer/subjects/cvs_avg35 corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35 dmrirc.example (configuration file) is attached to this e-mail. Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-05-27 22:57 GMT+09:00 Anastasia Yendiki : Hi Anri - I do not know what command line you ran and what your configuration file looks like, so it is very hard for me to suggest solutions. Best, a.y On Fri, 27 May 2016, Anri WATANABE wrote: Hi Anastasia, Thank you for your answer.
Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)
Hi there - I think I know what it is, but it's a problem that should be solved if you have the last tracula update. It means that your LANG environment variable needs to be set to en_US.UTF-8, which the update does for you. a.y On Tue, 5 Jul 2016, Lars M. Rimol wrote: Hi Anastasia, I have attached the dmri/bvals and dmri/bvec ("bvals"/"bvecs") and the dmri/dwi_orig.mghdti* files. I don't know if it's a problem but the generated bvec file has commas instead of full stop (0,832 instead of 0.832). The input file (attached: "bvec_rows") has full stop. Another thing is that the generated bvals file has an empty space at the end of the row, which is not there in the input file ("bvals_rows"). thank you! LMR Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals and dmri/bvecs files that get generated look fine too? a.y On Sat, 2 Jul 2016, Lars M. Rimol wrote: Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I do n't understand why, since both have the same number of rows (64). OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated Tracula and FSL (v 5.0.9). Error message: #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016 dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.n ii.gz -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 U TC 2015 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016 -- I also tried flipping the bvec/bval files, but got the same error. I don't know if there's anything wrong with the bval/bvec files, or if this error message is indicative of some other problem. Is the updated Tracula version only compatible with the dev version of FS? I have attached the bval/bvec files and the trac-all.log. --- The contents of the dmric file is: setenv SUBJECTS_DIR /media/lmr2/subjects/DTI set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot = /media/lmr2/subjects/DTI set dcmlist = ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv Thank you! yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header
You get the same error as trac-all because trac-all runs mri_convert. I'd send the mri_convert error in a new email with mri_convert somewhere in the title, so that someone else can help you. On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Also when I run mir_convert on the DICOMs I get the same error as the one I got when I used DICOMs : WARNING: file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/3T2/MR.1.3.12.2.1107.5.2.19. 45306.2014091812330393354083931 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header Any idea what this could be ? Thanks, Ismail On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail wrote: It says 1 … I don’t understand why I get that knowing that when I open the nifti I can go through the frames … Ismail On Jul 4, 2016, at 3:11 PM, Anastasia Yendiki wrote: I do not know why the dicoms do not work. When you run mri_info on your nifti, what is the number of frames that shows up? On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason. Also why the DICOMs wouldn’t work at the beginning ? Thanks, Ismail On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki wrote: Hi Ismail - You can see from the log file that the command that causes the error is this: mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out. a.y On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again, Ismail On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki wrote: Hi Ismail - It sounds like the error has to do with the nifti volume, not the bvecs/bvals. Can you send the log file from scripts/trac-all.log? Thanks, a.y On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all
Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header
I do not know why the dicoms do not work. When you run mri_info on your nifti, what is the number of frames that shows up? On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, This is what’s weird, my nifti volume contains 64 frames as my bvecs/bvals. So this shouldn’t be the reason. Also why the DICOMs wouldn’t work at the beginning ? Thanks, Ismail On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki wrote: Hi Ismail - You can see from the log file that the command that causes the error is this: mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out. a.y On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again, Ismail On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki wrote: Hi Ismail - It sounds like the error has to do with the nifti volume, not the bvecs/bvals. Can you send the log file from scripts/trac-all.log? Thanks, a.y On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error : WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368 0043 .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional space, but when the new bvecs and bvals are created, they seem messed up. I will attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used. On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki wrote: Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote: Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header
Hi Ismail - You can see from the log file that the command that causes the error is this: mri_convert --frame 31 /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi.nii.gz /Users/ismailkoubiyr/Documents/PFE/Tracula/out/3T5/dmri/dwi_frame31.nii.gz It's trying to extract the 32nd frame of your nifti file, but from the error message it looks like your nifti file doesn't have a 32nd frame. So either the nifti file has too few volumes, or the bvecs/bvals have too many lines. You'll have to figure that out. a.y On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, Here it is. But how could the problem be related to the nifti volume since I have errors when using the DICOMs too ? Thanks again, Ismail > On Jul 4, 2016, at 1:44 PM, Anastasia Yendiki wrote: > > > Hi Ismail - It sounds like the error has to do with the nifti volume, not the bvecs/bvals. Can you send the log file from scripts/trac-all.log? > > Thanks, > a.y > > On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: > >> Hi Anastasia, >> Thank you for getting back to me. >> Here are more details about my problem, I think it should help you >> understand more. >> I run trac-all -prep -c on some DICOM files but I had the following error : >> WARNING:file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.368 0043 >> .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII >> header >> has this file been anonymized? >> ERROR: cannot unpack mosiacs without ASCII header >> I also tried to de-mosiac the DICOMs, it gave me the same error. >> Then I converted the DICOMs into NIFTI, which allowed me not to get the >> previous error but something else weird happened. Now I get : >> ERROR: fMRIframe: frame >= nframes >> I checked the bvecs and bvals files, they seem normal, no additional space, >> but when the new bvecs and bvals are created, they seem messed up. I will >> attach you all the bvecs and bvals I used and the ones I get too. >> Ideally, the DICOMs should work fine but I have no idea why I get these >> errors. >> The bvecs and bvals are obtained from dcm2nii and then corrected to avoid >> any additional space. >> Thank you in advance for your help. >> Best, >> Ismail >> P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used. >> >> On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki >> wrote: >> Hi Ismail - Are you passing the nifti volume as input to trac-all? >> It's >> hard to tell without looking at your configuration file. >> Best, >> a.y >> On Tue, 28 Jun 2016, Koubiyr, Ismail wrote: >> >> Hi everyone, >> >> I have some problems trying to run TRACULA on some DWI >> data. It is a mosaic Siemens DWI. I first converted the >> DICOM files with dcm2nii to get the bvec and bval files. >> Then I run the trac-all -prep -c command and I get the >> following error : >> >> WARNING: file /My/path/to/dicom does not contain a Siemens >> ASCII header >> has this file been anonymized? >> ERROR: cannot unpack mosiacs without ASCII header >> >> I tried to unpack the mosaics with gdcmtar, but I got the >> same error. >> >> Thank you in advance for your help, >> >> Ismail >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header
Hi Ismail - It sounds like the error has to do with the nifti volume, not the bvecs/bvals. Can you send the log file from scripts/trac-all.log? Thanks, a.y On Mon, 4 Jul 2016, Koubiyr, Ismail wrote: Hi Anastasia, Thank you for getting back to me. Here are more details about my problem, I think it should help you understand more. I run trac-all -prep -c on some DICOM files but I had the following error : WARNING: file/Users/ismailkoubiyr/Documents/PFE/Tracula/dti/SER_5/MR.1.2.826.0.1.3680043 .6.8878.22551.20150806120704.648.1017 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I also tried to de-mosiac the DICOMs, it gave me the same error. Then I converted the DICOMs into NIFTI, which allowed me not to get the previous error but something else weird happened. Now I get : ERROR: fMRIframe: frame >= nframes I checked the bvecs and bvals files, they seem normal, no additional space, but when the new bvecs and bvals are created, they seem messed up. I will attach you all the bvecs and bvals I used and the ones I get too. Ideally, the DICOMs should work fine but I have no idea why I get these errors. The bvecs and bvals are obtained from dcm2nii and then corrected to avoid any additional space. Thank you in advance for your help. Best, Ismail P.S : 3T2_bvecs.txt and 3T2_bvals.txt are the original files used. On Jul 4, 2016, at 3:32 AM, Anastasia Yendiki wrote: Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote: Hi everyone, I have some problems trying to run TRACULA on some DWI data. It is a mosaic Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec and bval files. Then I run the trac-all -prep -c command and I get the following error : WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I tried to unpack the mosaics with gdcmtar, but I got the same error. Thank you in advance for your help, Ismail ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] longitudinal tracula
Hi Michael - There is no bvec file associated with the base template. The base template is a structural (the median of a subject's structural time points) and not a diffusion scan. The way you'd want to account for different amounts of motion across subjects in a cross-sectional analysis, you'd probably want to account for different changes in motion in a longitudinal study. Whether you'd also want to discard data is an open question. a.y On Mon, 4 Jul 2016, Harms, Michael wrote: So, what bvec/bvec file should be associated with the BASE scan? It isn’t clear to me how the bvec/bval in the BASE scan get used in trac-paths. I see the point of your note of caution, but unless someone moved the same amount (and for the same frames) for their sessions in a longitudinal study, the same issue applies, even if you use all frames “as is”. In that case, the potential bias would be due to using data of differing quality across sessions. In a sense, we are just making the issue explicit by discarding bad frames as part of a QC step. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 7/4/16, 2:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Michael - Indeed it should not be too difficult to add the feature of specifying the b-value table for each scan and I can add this in the next version. However, I would be a bit careful with removing different DWI volumes for different time points. The acquisition should be as consistent as possible across time points. If you find that there's a longitudinal change, would this be because there were different directions/b-values in each time point or because of an actual change in the brain? I suppose that, unless there's a systematic bias, you might expect that these changes will be in different directions for different subjects and would then average out. But it's a tricky issue. Best, a.y On Fri, 1 Jul 2016, Harms, Michael wrote: Hi Anastasia, Looking through the trac-preproc and trac-paths scripts, it is now clear to me that all the time points for a given subject have to be contained/specified within the same dmrirc configuration file in order to implement a longitudinal TRACULA analysis. So, I've answered my previous question in that regard. The challenge in our case is that we have separately pre-processed the dMRI data for each subject and time point, removing bad frames/volumes (using the DTIPrep QA tool). Thus, the bvecs/bvals are not identical for all the time points of a given subject. We can specify the bvec file for each subject/time point using the bveclist configuration parameter. But there is no analog available for bvals, since only a single bvalfile can be specified. I see that this issue has been raised in a couple other posts relatively recently (2015): https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html but no working solution was provided at that time. I’m wondering if there is perhaps now a development version of TRACULA that supports a “bvallist” capability? If not, it doesn’t look like it would be too difficult to modify trac-all to include that capability (modeling after what is already in trac-all for the bveclist/bvecfile stuff). But, in that case, it isn’t immediately clear to me if there are other downstream “gotchas” in the preproc, paths, or stats stage specific scripts/binaries that would need modifications as well. [I don’t see anything in the sections related to the BASE-specific processing in trac-preproc involving bvals/bvecs, so think we are fine there. But it is harder for me to tell what is going on in trac-paths]. thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of "Harms, Michael" Reply-To: Freesurfer support list Date: Wednesday, June 29, 2016 at 5:00 PM To: Freesurfer support list Subject: [Freesurfer] longitudinal tracula Hi, When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file? My initial thought was “no”, that it would be fine to run one scan wave per subject per dmrirc file (as long as the “baselist” variable is set appropriately for each scan wave and subject). But looking at the ‘trac-all’ script, I see if ($#baselist == 0) then#--->>> A single time point
Re: [Freesurfer] trac-all error (bvecs and bvals don't have same number of entries)
Hi Lars - At first glance, these files look fine to me. Do the dmri/bvals and dmri/bvecs files that get generated look fine too? a.y On Sat, 2 Jul 2016, Lars M. Rimol wrote: Hi, Trying to run trac-all -c dmric_file -prep, I get an error message stating that there are different numbers of entries in the bval and bvec files. I don't understand why, since both have the same number of rows (64). OS = Ubuntu 14.04.4 Software: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0; I have updated Tracula and FSL (v 5.0.9). Error message: #@# Tensor fit fr. 01. juli 19:20:29 +0200 2016 dtifit -k /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dwi.nii.gz -m /media/lmr2/subjects/DTI/tracula_2016/4_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -r /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvecs -b /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/bvals -o /media/lmr2/subjects/DTI/tracula_2016/4_FS/dmri/dtifit Error: bvecs and bvals don't have the same number of entries Linux dmed4870 3.19.0-31-generic #36~14.04.1-Ubuntu SMP Thu Oct 8 10:21:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at fr. 01. juli 19:20:30 +0200 2016 -- I also tried flipping the bvec/bval files, but got the same error. I don't know if there's anything wrong with the bval/bvec files, or if this error message is indicative of some other problem. Is the updated Tracula version only compatible with the dev version of FS? I have attached the bval/bvec files and the trac-all.log. --- The contents of the dmric file is: setenv SUBJECTS_DIR /media/lmr2/subjects/DTI set dtroot = /media/lmr2/subjects/DTI/tracula_2016_nativerows set subjlist = (4_FS) set dcmroot = /media/lmr2/subjects/DTI set dcmlist = ( 4/5/1.dcm ) set bvalfile = /media/lmr2/subjects/DTI/bvals_rows.csv set bvecfile = /media/lmr2/subjects/DTI/bvec_rows.csv Thank you! yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA group stats visualization
Hi Derek - Are you by any chance using the dev version of freeview? a.y On Fri, 1 Jul 2016, Derek Pisner wrote: Dear Anastasia, I am running into an issue with the trac-all -stat option on our longitudinal TRACULA data. Everything runs smoothly through all earlier stages, and I checked individual subjects' merged outputs in freeview with -tv mode. Everything looks fine. Also, then when I run trac-all -c dmric_config -stat, everything finishes without error. But then when I open the results with the command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w /data/blt/TRACULA/tractography_output/stats.long/*.path.mean.txt I get the image seen in the attached .png file. Any idea what might be causing this? Many thanks in advance for you help. Best, Derek ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] longitudinal tracula
Hi Michael - Indeed it should not be too difficult to add the feature of specifying the b-value table for each scan and I can add this in the next version. However, I would be a bit careful with removing different DWI volumes for different time points. The acquisition should be as consistent as possible across time points. If you find that there's a longitudinal change, would this be because there were different directions/b-values in each time point or because of an actual change in the brain? I suppose that, unless there's a systematic bias, you might expect that these changes will be in different directions for different subjects and would then average out. But it's a tricky issue. Best, a.y On Fri, 1 Jul 2016, Harms, Michael wrote: Hi Anastasia, Looking through the trac-preproc and trac-paths scripts, it is now clear to me that all the time points for a given subject have to be contained/specified within the same dmrirc configuration file in order to implement a longitudinal TRACULA analysis. So, I've answered my previous question in that regard. The challenge in our case is that we have separately pre-processed the dMRI data for each subject and time point, removing bad frames/volumes (using the DTIPrep QA tool). Thus, the bvecs/bvals are not identical for all the time points of a given subject. We can specify the bvec file for each subject/time point using the bveclist configuration parameter. But there is no analog available for bvals, since only a single bvalfile can be specified. I see that this issue has been raised in a couple other posts relatively recently (2015): https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html but no working solution was provided at that time. I’m wondering if there is perhaps now a development version of TRACULA that supports a “bvallist” capability? If not, it doesn’t look like it would be too difficult to modify trac-all to include that capability (modeling after what is already in trac-all for the bveclist/bvecfile stuff). But, in that case, it isn’t immediately clear to me if there are other downstream “gotchas” in the preproc, paths, or stats stage specific scripts/binaries that would need modifications as well. [I don’t see anything in the sections related to the BASE-specific processing in trac-preproc involving bvals/bvecs, so think we are fine there. But it is harder for me to tell what is going on in trac-paths]. thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of "Harms, Michael" Reply-To: Freesurfer support list Date: Wednesday, June 29, 2016 at 5:00 PM To: Freesurfer support list Subject: [Freesurfer] longitudinal tracula Hi, When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file? My initial thought was “no”, that it would be fine to run one scan wave per subject per dmrirc file (as long as the “baselist” variable is set appropriately for each scan wave and subject). But looking at the ‘trac-all’ script, I see if ($#baselist == 0) then#--->>> A single time point for each subject … else#--->>> Multiple time points for each subject … So, I’m wondering why different sections in the code would be necessary if in fact it is ok to process a single scan wave per dmrirc file. thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosu
Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header
Hi Ismail - Are you passing the nifti volume as input to trac-all? It's hard to tell without looking at your configuration file. Best, a.y On Tue, 28 Jun 2016, Koubiyr, Ismail wrote: > Hi everyone, > > I have some problems trying to run TRACULA on some DWI data. It is a mosaic > Siemens DWI. I first converted the DICOM files with dcm2nii to get the bvec > and bval files. > Then I run the trac-all -prep -c command and I get the following error : > > WARNING: file /My/path/to/dicom does not contain a Siemens ASCII header > has this file been anonymized? > ERROR: cannot unpack mosiacs without ASCII header > > I tried to unpack the mosaics with gdcmtar, but I got the same error. > > Thank you in advance for your help, > > Ismail > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] tracula not work
Hi Yang - Have you followed the instructions on how to set up the freesurfer environment? https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration Best, a.y On Mon, 13 Jun 2016, yangfuxing wrote: Hi professor?? When I finished setting up the configuration file "dmrirc", type "trac-all -c dmrirc"in the terminal ,it return "FSLDIR: Undefined variable", how can I solve it?Thank you. Best, yang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: TRACULA stat extraction issue
Hi Shashwath - It looks like you have modified the directory structure of the output files. Normally the dpath/ directory is right under the directory with subject's name. From your file of inputs, it looks like you've created some other subdirectories and now dpath/ is a few levels down the hierarchy. I'd recommend reverting to the original structure that the commands expect. Best, a.y On Fri, 10 Jun 2016, Shashwath Meda wrote: Dear Group - I seem to have run into an issue when attempting to assimilate the averaged pathway information from TRACULA into a group table. I have attached my input list of paths and my output table for one of the tracts. The below is the command that i have used but as you can see the values in my final table are all from one subject (just replicated) despite my input list having paths from different subjects, Has anyone encountered a similar situation? tractstats2table --load-pathstats-from-file fmajor_PP_avg33_mni_bbr.txt --overall --tablefile fmajor_PP_avg33_mni_bbr.table -- Best, Shashwath ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] About TRACULA
Hi Yang - TRACULA does not assume that the shape, size, or integrity of the tracts is the same in the study subjects as in the atlas subjects. It just assumes that the relative position of the tracts with respect to the cortical and subcortical segmentation labels from freesurfer. For example, does tract X go lateral to the thalamus or superior to the thalamus, and does this happen in the beginning, end, or 2/3 along the length of tract X? If these general relationships are preserved, and if the cortical and subcortical segmentation can be reconstructed in the study subjects, then TRACULA should work. Again, the best way to know if TRACULA will work is to run it on a couple of representative subjects. I may have written every line of code in it, I can explain how it works, but even I can't predict how it'll do on every single data set out there that I haven't even seen :) Best, a.y On Thu, 2 Jun 2016, ?? wrote: Hi, To be specific, I'm trying to reconstruct arcuate fasciculus (refer to SLFT according to your paper 2011) in patients who suffered from frontal or temporal or parietal gliomas. I noticed that TRACULA was used to study neuropsychiatry and neurodegeneration diseases, such as schizophrenia, autism etc. When it comes to organic diseases, like brain tumor, white matter structures may be pushed or deformed due to mass effect. So my question is should I involve the patients in the training set? What can I do to succeed in reconstruction of arcuate fasciculus using TRACULA in my research? Thanks for your time. BW, yang -- Original -- From: "ayendiki";; Date: Jun 2, 2016 To: "Freesurfer support list"; Subject: Re: [Freesurfer] About TRACULA Hi - It's hard to predict in advance what will happen without trying it out. A lot will depend on the size/position/nature of the tumor. Some tumor patients will go through just fine, other will have issues. If the freesurfer segmentation works, then tracula will work too. Best, a.y On Thu, 2 Jun 2016, yangfuxing wrote: > Dear professor, > I'm a postgraduate of neurosurgery. Recently, I'm interested in cortical > parcellation and subcortical segmentation using freesurfer. In my study, all > patients have brain tumors. So I begin to wonder if "recon-all" can still be > applied to these subjects, or in other word, is it possible that > freesurfer's automated brain segmentation could be applied to brain tumor > patients because their normal structures were changed? If I just run it > regularly according to fswiki, would the outcome be accurate? > Second question is about automatic tractography using TRACULA. > Similarly, I'd like to use "trac-all" to reconstruct arcuate fasciculus in > patients with brain tumor, is it possible? How can I set up the > configuration? Hope to hear from you soon. Best wishes! > Sincerely > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] About TRACULA
Hi - It's hard to predict in advance what will happen without trying it out. A lot will depend on the size/position/nature of the tumor. Some tumor patients will go through just fine, other will have issues. If the freesurfer segmentation works, then tracula will work too. Best, a.y On Thu, 2 Jun 2016, yangfuxing wrote: Dear professor, I'm a postgraduate of neurosurgery. Recently, I'm interested in cortical parcellation and subcortical segmentation using freesurfer. In my study, all patients have brain tumors. So I begin to wonder if "recon-all" can still be applied to these subjects, or in other word, is it possible that freesurfer's automated brain segmentation could be applied to brain tumor patients because their normal structures were changed? If I just run it regularly according to fswiki, would the outcome be accurate? Second question is about automatic tractography using TRACULA. Similarly, I'd like to use "trac-all" to reconstruct arcuate fasciculus in patients with brain tumor, is it possible? How can I set up the configuration? Hope to hear from you soon. Best wishes! Sincerely ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coordinates in TRACULA group analysis
Thanks, Anri. So the previous steps seem to have run fine. Are there any .log files created in the stats/ folder, which is created by trac-all -stat? On Wed, 1 Jun 2016, Anri WATANABE wrote: Hi Anastasia, This is a /scripts/trac-all.log of one subject of the group. Thanks, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-05-31 22:55 GMT+09:00 Anastasia Yendiki : Hi Anri - Can you also send your log file (scripts/trac-all.log)? I'll need to see what exactly was running when the error occurred. Thanks! a.y On Sat, 28 May 2016, Anri WATANABE wrote: Hello Anastasia,sorry for few information and let me tell you command and error log. Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example Error log: Loading output reference volume from /Applications/freesurfer/subjects/cvs_avg35 corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35 dmrirc.example (configuration file) is attached to this e-mail. Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-05-27 22:57 GMT+09:00 Anastasia Yendiki : Hi Anri - I do not know what command line you ran and what your configuration file looks like, so it is very hard for me to suggest solutions. Best, a.y On Fri, 27 May 2016, Anri WATANABE wrote: Hi Anastasia, Thank you for your answer. There aren't stats/*.path.mean.txt files and terminal says 'Could not read /Applications/freesurfer/subjects/cvs_avg35.' I checked /Application/freesurfer/subjects/cvs_avg35 folder and couldn't find COR-.info file. Could you tell me any resolutions, please? Thanks, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-05-21 6:48 GMT+09:00 Anastasia Yendiki : Hi Anri - The FA values are extracted in the native space of each subject, which is why those are the only coordinates that you see. If you want to display the results of your analysis on an average path, after running trac-all -stat, you can use the stats/*.path.mean.txt files (see also the last part of the TRACULA tutorial). Best, a.y On Wed, 18 May 2016, Anri WATANABE wrote: Dear experts, I use TRACULA to examine a measure (FA) at each voxel in one pathway. pathstats.byvoxel.txt files show coordinates in native space and after converting those the new files don't show any coordinates which are in MNI space. Could you tell me how can I know MNI coordinate values? Thank you! Regards,
Re: [Freesurfer] Tracula skip steps
The input needs to be the diffusion-weighted images, not the FA, MD, etc. There should be as many volumes in this input nifti as there are b-values in bval file and gradient vectors in the bvec file. The image registration, tractography, etc etc is performed on the diffusion-weighted images, not on the FA, MD, etc. The FA, MD, etc are used only in the very end, to extract FA, MD, etc for each tract. But to get the tracts in the first place, you need the images. On Tue, 31 May 2016, Jacobs H (NP) wrote: Yes, each nifti contains one volume. I have different nifti’s for the different metrics (FA, MD,..) Is there a way I can use the trac-all on these files? On 5/31/16, 9:26 PM, "Anastasia Yendiki" wrote: Some of the errors make me suspect that your input DWI files contain only one volume. Could this be the case? On Tue, 31 May 2016, Jacobs H (NP) wrote: Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 gives the same error. Enclosed is the config file. Thank you so much Heidi On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look. Best, a.y On Tue, 31 May 2016, Jacobs H (NP) wrote: Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration. On Tue, 31 May 2016, Jacobs H (NP) wrote: Dear Anastasia, Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images. Thanks Best Heidi On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way. Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks! a.y On Tue, 31 May 2016, Jacobs H (NP) wrote: Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: / dtifit_FA.nii.gz I have also filled in the configuration file, canceling out the things I don¹t need and then I tried to run: Trac-all intra c Unfortunately, it does not work, it says: dcmlist: subscript out of range I do not have the original filesŠ is there a way that I can get the script working? Many thanks. Heidi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula skip steps
Some of the errors make me suspect that your input DWI files contain only one volume. Could this be the case? On Tue, 31 May 2016, Jacobs H (NP) wrote: Hmm, weird, as I put a # in front of it. Putting the eddy current to 0 gives the same error. Enclosed is the config file. Thank you so much Heidi On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look. Best, a.y On Tue, 31 May 2016, Jacobs H (NP) wrote: Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration. On Tue, 31 May 2016, Jacobs H (NP) wrote: Dear Anastasia, Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images. Thanks Best Heidi On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way. Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks! a.y On Tue, 31 May 2016, Jacobs H (NP) wrote: Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: / dtifit_FA.nii.gz I have also filled in the configuration file, canceling out the things I don¹t need and then I tried to run: Trac-all intra c Unfortunately, it does not work, it says: dcmlist: subscript out of range I do not have the original filesŠ is there a way that I can get the script working? Many thanks. Heidi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula skip steps
Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (see example config file). Based on your log file, it looks like you haven't turned off the eddy current compensation, because it's trying to run it. If you attach your config file, I'll take a look. Best, a.y On Tue, 31 May 2016, Jacobs H (NP) wrote: Thanks! I tried to adapt the configuration file and it got a bit further, but then crashes again. Not sure why? I have added the log file, so that maybe you could have a look at what is happening? Also, how does the trac-all command knows where to find the T1 data? Thanks Heidi On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration. On Tue, 31 May 2016, Jacobs H (NP) wrote: Dear Anastasia, Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images. Thanks Best Heidi On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way. Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks! a.y On Tue, 31 May 2016, Jacobs H (NP) wrote: Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: / dtifit_FA.nii.gz I have also filled in the configuration file, canceling out the things I don¹t need and then I tried to run: Trac-all intra c Unfortunately, it does not work, it says: dcmlist: subscript out of range I do not have the original filesŠ is there a way that I can get the script working? Many thanks. Heidi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula skip steps
No, it should be pointed to the DWI data, which can be corrected niftis instead of the original dicoms. I would recommend turning off all the corrections in the configuration file, and then running everything without skipping steps. This will create all the files that are expected to be there for the registration. On Tue, 31 May 2016, Jacobs H (NP) wrote: Dear Anastasia, Thanks for the feedback. So, does this mean that the dcm root should be pointed towards the T1¹s? I have the FreeSurfer recon-all output in a different folder. Enclosed is the log file (of one subject) and the configuration file. You will see that I tried the inter and intra option, because I thought that for the inter it would not need anything else than the MNI template and the DTI images. Thanks Best Heidi On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" wrote: Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way. Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks! a.y On Tue, 31 May 2016, Jacobs H (NP) wrote: Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: / dtifit_FA.nii.gz I have also filled in the configuration file, canceling out the things I don¹t need and then I tried to run: Trac-all intra c Unfortunately, it does not work, it says: dcmlist: subscript out of range I do not have the original filesŠ is there a way that I can get the script working? Many thanks. Heidi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula skip steps
Hi Heidi - The intra-subject registration step that you're trying to run registers your subject's DWI and T1 images. It expects to find those images. It doesn't use the FA, MD, etc in any way. Did the log file get created in scripts/trac-all.log? If so, can you please send that file and your configuration file? Thanks! a.y On Tue, 31 May 2016, Jacobs H (NP) wrote: Dear FreeSurfers, The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, L3,..) in nifti format. On this data I would like to start tracula starting from step 1.3. I have organized the data as mentioned on the wiki: For example: / dtifit_FA.nii.gz I have also filled in the configuration file, canceling out the things I don’t need and then I tried to run: Trac-all –intra –c Unfortunately, it does not work, it says: dcmlist: subscript out of range I do not have the original files… is there a way that I can get the script working? Many thanks. Heidi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coordinates in TRACULA group analysis
Hi Anri - Can you also send your log file (scripts/trac-all.log)? I'll need to see what exactly was running when the error occurred. Thanks! a.y On Sat, 28 May 2016, Anri WATANABE wrote: Hello Anastasia,sorry for few information and let me tell you command and error log. Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example Error log: Loading output reference volume from /Applications/freesurfer/subjects/cvs_avg35 corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35 dmrirc.example (configuration file) is attached to this e-mail. Thanks in advance, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-05-27 22:57 GMT+09:00 Anastasia Yendiki : Hi Anri - I do not know what command line you ran and what your configuration file looks like, so it is very hard for me to suggest solutions. Best, a.y On Fri, 27 May 2016, Anri WATANABE wrote: Hi Anastasia, Thank you for your answer. There aren't stats/*.path.mean.txt files and terminal says 'Could not read /Applications/freesurfer/subjects/cvs_avg35.' I checked /Application/freesurfer/subjects/cvs_avg35 folder and couldn't find COR-.info file. Could you tell me any resolutions, please? Thanks, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-05-21 6:48 GMT+09:00 Anastasia Yendiki : Hi Anri - The FA values are extracted in the native space of each subject, which is why those are the only coordinates that you see. If you want to display the results of your analysis on an average path, after running trac-all -stat, you can use the stats/*.path.mean.txt files (see also the last part of the TRACULA tutorial). Best, a.y On Wed, 18 May 2016, Anri WATANABE wrote: Dear experts, I use TRACULA to examine a measure (FA) at each voxel in one pathway. pathstats.byvoxel.txt files show coordinates in native space and after converting those the new files don't show any coordinates which are in MNI space. Could you tell me how can I know MNI coordinate values? Thank you! Regards, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains pati
Re: [Freesurfer] Coordinates in TRACULA group analysis
Hi Anri - I do not know what command line you ran and what your configuration file looks like, so it is very hard for me to suggest solutions. Best, a.y On Fri, 27 May 2016, Anri WATANABE wrote: Hi Anastasia, Thank you for your answer. There aren't stats/*.path.mean.txt files and terminal says 'Could not read /Applications/freesurfer/subjects/cvs_avg35.' I checked /Application/freesurfer/subjects/cvs_avg35 folder and couldn't find COR-.info file. Could you tell me any resolutions, please? Thanks, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-05-21 6:48 GMT+09:00 Anastasia Yendiki : Hi Anri - The FA values are extracted in the native space of each subject, which is why those are the only coordinates that you see. If you want to display the results of your analysis on an average path, after running trac-all -stat, you can use the stats/*.path.mean.txt files (see also the last part of the TRACULA tutorial). Best, a.y On Wed, 18 May 2016, Anri WATANABE wrote: Dear experts, I use TRACULA to examine a measure (FA) at each voxel in one pathway. pathstats.byvoxel.txt files show coordinates in native space and after converting those the new files don't show any coordinates which are in MNI space. Could you tell me how can I know MNI coordinate values? Thank you! Regards, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] DTI error
Hi Jasmin - On my screen the dash "-" symbol before the "c" looks different than the one before "path". I'd check if you are indeed typing a plain "-c". Best, a.y On Wed, 25 May 2016, Jasmin Alves wrote: Hi Anastasia, I am still receiving the following error message when I run a different participant doing, trac-all -path –c dmrirc1_sim.txt: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt If you have any ideas for what i can try it would be very appreciated! Thanks! Jasmin On Sun, May 22, 2016 at 9:07 PM, Jasmin Alves wrote: Correct. On Sunday, May 22, 2016, Anastasia Yendiki wrote: No idea, sorry. You used the -c option with the previous steps of trac-all and didn't see this error, correct? On Sun, 22 May 2016, Jasmin Alves wrote: Hi Anastasia, Perhaps I was asking for advice regarding the wrong step in trac-all, do you have any ideas why I am still receiving the following error: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt This occurs when I do trac-all -path –c dmrirc1_sim.txt I tried looking at posts from previous mailing lists, and found no match to this problem. Thank you, Jasmin On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki wrote: Ok, then you can ignore the error that you see when you run the bedpost step. `On Sun, 22 May 2016, Jasmin Alves wrote: Sorry for the mix-up. All of the bedpost output files are generated as well both 1 and 2 of each file. On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki wrote: These are output files from the -prep step. I'm asking about output files from the bedpost step, since that's where you're encountering the error. https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard .edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp&d=DQIDaQ&c=clK7kQUTWt AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7c1gaW5UpDUs-D f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8&s=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA &e= What's in the dmri.bedpostX/ directory? On Sun, 22 May 2016, Jasmin Alves wrote: Output files are being generated, ie. 1. dtifit_FA.nii.gz - Fractional Anisotropy 2. dtifit_MD.nii.gz - Mean Diffusivity 3. dtifit_MO.nii.gz - Mode of the Anisotropy 4. dtifit_S0.nii.gz - Non-Diffusion weighted image 5. dtifit_L1.nii.gz - Primary Eigenvalue 6. dtifit_L2.nii.gz - Secondary Eigenvalue 7. dtifit_L3.nii.gz - Tertiary Eigenvalue 8. dtifit_V1.nii.gz - Primary Eigenvector 9. dtifit_V2.nii.gz - Secondary Eigenvector 10. dtifit_V3.nii.gz - Tertiary Eigenvector But it seems the bedpost process gets cut short and then, the trac-all path step won't work. I have ran it a few times and the bedpost step ends at the same point. On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki wrote: But do you see the output files from the previous step? The outputs from each step are described on the wiki. On Sun, 22 May 2016, Jasmin Alves wrote: Hi Anastasia, Thank you for the reply, when I do just let it run,
Re: [Freesurfer] DTI error
No idea, sorry. You used the -c option with the previous steps of trac-all and didn't see this error, correct? On Sun, 22 May 2016, Jasmin Alves wrote: Hi Anastasia, Perhaps I was asking for advice regarding the wrong step in trac-all, do you have any ideas why I am still receiving the following error: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt This occurs when I do trac-all -path –c dmrirc1_sim.txt I tried looking at posts from previous mailing lists, and found no match to this problem. Thank you, Jasmin On Sun, May 22, 2016 at 5:53 PM, Anastasia Yendiki wrote: Ok, then you can ignore the error that you see when you run the bedpost step. `On Sun, 22 May 2016, Jasmin Alves wrote: Sorry for the mix-up. All of the bedpost output files are generated as well both 1 and 2 of each file. On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki wrote: These are output files from the -prep step. I'm asking about output files from the bedpost step, since that's where you're encountering the error. https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard .edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp&d=DQIDaQ&c=clK7kQUTWt AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7c1gaW5UpDUs-D f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8&s=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA &e= What's in the dmri.bedpostX/ directory? On Sun, 22 May 2016, Jasmin Alves wrote: Output files are being generated, ie. 1. dtifit_FA.nii.gz - Fractional Anisotropy 2. dtifit_MD.nii.gz - Mean Diffusivity 3. dtifit_MO.nii.gz - Mode of the Anisotropy 4. dtifit_S0.nii.gz - Non-Diffusion weighted image 5. dtifit_L1.nii.gz - Primary Eigenvalue 6. dtifit_L2.nii.gz - Secondary Eigenvalue 7. dtifit_L3.nii.gz - Tertiary Eigenvalue 8. dtifit_V1.nii.gz - Primary Eigenvector 9. dtifit_V2.nii.gz - Secondary Eigenvector 10. dtifit_V3.nii.gz - Tertiary Eigenvector But it seems the bedpost process gets cut short and then, the trac-all path step won't work. I have ran it a few times and the bedpost step ends at the same point. On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki wrote: But do you see the output files from the previous step? The outputs from each step are described on the wiki. On Sun, 22 May 2016, Jasmin Alves wrote: Hi Anastasia, Thank you for the reply, when I do just let it run, I get the following error when I try to do trac-all -path –c dmrirc1_sim.txt I get the following error: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt Thanks, Jasmin On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki wrote: Hi Jasmin - Check if things are running despite that error. Are output files being generated? a.y On Sat, 21 May 2016, Jasmin Alves wrote: Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin AlvesPredoctoral Student
Re: [Freesurfer] DTI error
Ok, then you can ignore the error that you see when you run the bedpost step. `On Sun, 22 May 2016, Jasmin Alves wrote: Sorry for the mix-up. All of the bedpost output files are generated as well both 1 and 2 of each file. On Sun, May 22, 2016 at 4:22 PM, Anastasia Yendiki wrote: These are output files from the -prep step. I'm asking about output files from the bedpost step, since that's where you're encountering the error. https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard .edu_fswiki_trac-2Dall-23Outputsfromtrac-2Dall-2Dbedp&d=DQIDaQ&c=clK7kQUTWt AVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=7c1gaW5UpDUs-D f4uqLGaiN1YKi8WpD7PUUFUH_Yh_8&s=PDchguGtZxsQtn6Ikrgq51EI2N8a2zv32ihUs8-gVaA &e= What's in the dmri.bedpostX/ directory? On Sun, 22 May 2016, Jasmin Alves wrote: Output files are being generated, ie. 1. dtifit_FA.nii.gz - Fractional Anisotropy 2. dtifit_MD.nii.gz - Mean Diffusivity 3. dtifit_MO.nii.gz - Mode of the Anisotropy 4. dtifit_S0.nii.gz - Non-Diffusion weighted image 5. dtifit_L1.nii.gz - Primary Eigenvalue 6. dtifit_L2.nii.gz - Secondary Eigenvalue 7. dtifit_L3.nii.gz - Tertiary Eigenvalue 8. dtifit_V1.nii.gz - Primary Eigenvector 9. dtifit_V2.nii.gz - Secondary Eigenvector 10. dtifit_V3.nii.gz - Tertiary Eigenvector But it seems the bedpost process gets cut short and then, the trac-all path step won't work. I have ran it a few times and the bedpost step ends at the same point. On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki wrote: But do you see the output files from the previous step? The outputs from each step are described on the wiki. On Sun, 22 May 2016, Jasmin Alves wrote: Hi Anastasia, Thank you for the reply, when I do just let it run, I get the following error when I try to do trac-all -path –c dmrirc1_sim.txt I get the following error: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt Thanks, Jasmin On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki wrote: Hi Jasmin - Check if things are running despite that error. Are output files being generated? a.y On Sat, 21 May 2016, Jasmin Alves wrote: Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYv Jp8mKI&s=fkP_flwCTRv-7FzQB1kw0eRwApBybsAjJNxNF8VH9RQ&e= The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail
Re: [Freesurfer] DTI error
These are output files from the -prep step. I'm asking about output files from the bedpost step, since that's where you're encountering the error. https://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Outputsfromtrac-all-bedp What's in the dmri.bedpostX/ directory? On Sun, 22 May 2016, Jasmin Alves wrote: Output files are being generated, ie. 1. dtifit_FA.nii.gz - Fractional Anisotropy 2. dtifit_MD.nii.gz - Mean Diffusivity 3. dtifit_MO.nii.gz - Mode of the Anisotropy 4. dtifit_S0.nii.gz - Non-Diffusion weighted image 5. dtifit_L1.nii.gz - Primary Eigenvalue 6. dtifit_L2.nii.gz - Secondary Eigenvalue 7. dtifit_L3.nii.gz - Tertiary Eigenvalue 8. dtifit_V1.nii.gz - Primary Eigenvector 9. dtifit_V2.nii.gz - Secondary Eigenvector 10. dtifit_V3.nii.gz - Tertiary Eigenvector But it seems the bedpost process gets cut short and then, the trac-all path step won't work. I have ran it a few times and the bedpost step ends at the same point. On Sun, May 22, 2016 at 3:24 PM, Anastasia Yendiki wrote: But do you see the output files from the previous step? The outputs from each step are described on the wiki. On Sun, 22 May 2016, Jasmin Alves wrote: Hi Anastasia, Thank you for the reply, when I do just let it run, I get the following error when I try to do trac-all -path –c dmrirc1_sim.txt I get the following error: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt Thanks, Jasmin On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki wrote: Hi Jasmin - Check if things are running despite that error. Are output files being generated? a.y On Sat, 21 May 2016, Jasmin Alves wrote: Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYv Jp8mKI&s=fkP_flwCTRv-7FzQB1kw0eRwApBybsAjJNxNF8VH9RQ&e= The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli anceline&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0 KTyqa6rNRHLug&m=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYvJp8mKI&s=ZCxo2mqb7_uBl K06A4PzG2Oc3tXOOfY5nkuRQDxr1-g&e= . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=KiW0HwopUPkuxl00iNmJ-d2_v8Lvm5ziYpz8r e5nRJg&s=BsW_UFqBiIvAMznFD1XkPkffaeZXmAgRB1Q1k-oulXs&e= The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_c
Re: [Freesurfer] DTI error
But do you see the output files from the previous step? The outputs from each step are described on the wiki. On Sun, 22 May 2016, Jasmin Alves wrote: Hi Anastasia, Thank you for the reply, when I do just let it run, I get the following error when I try to do trac-all -path –c dmrirc1_sim.txt I get the following error: ERROR: flag –c unrecognized -path –c dmrirc1_sim.txt Thanks, Jasmin On Sun, May 22, 2016 at 1:51 AM, Anastasia Yendiki wrote: Hi Jasmin - Check if things are running despite that error. Are output files being generated? a.y On Sat, 21 May 2016, Jasmin Alves wrote: Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e du_mailman_listinfo_freesurfer&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8 p7CSfnc_gI&r=LH_W279i0KTyqa6rNRHLug&m=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYv Jp8mKI&s=fkP_flwCTRv-7FzQB1kw0eRwApBybsAjJNxNF8VH9RQ&e= The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli anceline&d=DQIBAg&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=LH_W279i0 KTyqa6rNRHLug&m=_YHMcYTHXxIXmxZsQ6qCykG0PXDj2RSyadSYvJp8mKI&s=ZCxo2mqb7_uBl K06A4PzG2Oc3tXOOfY5nkuRQDxr1-g&e= . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] DTI error
Hi Jasmin - Check if things are running despite that error. Are output files being generated? a.y On Sat, 21 May 2016, Jasmin Alves wrote: Dear Freesurfer, While doing the bedpost step for TRAC-all ( trac-all -bedp -c dmrirc1_sim.txt) I received the following error: /Applications/freesurfer/bin/bedpostx_mgh: line 345: kill: (51042) - No such process Any ideas? Thank you, Jasmin Jasmin AlvesPredoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Mult-Shell Tracula Help
Hi Kristina - You can enter nifti DWI volumes in the configuration file (or any other format that mri_convert can recognize). You should do the entire processing from scratch (including bedpost) using the concatenated data. Best, a.y On Fri, 20 May 2016, Kristina Jelinkova wrote: > Hi Anastasia, > > Thank you for your response. Yes, we have created the concatenated DWIs and > bvec/bval files that we have gotten after running each of the sequences > separately from trac-all. How can we run these concatenated nii.gz mages > through the ball-and-stick model fit (I'm assuming the configuration file > only looks for dcm images)? Would we also need to run bedpostX again > separately with the concatenated images? > > Thanks again for your help! > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: Friday, May 20, 2016 3:52:02 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] Mult-Shell Tracula Help > > Hi Kristina - I'm assuming the 2 data sets were acquired in the same > session and with the same acquisition parameters, other than the b-values? > Then you can just concatenate the DWIs from the 2 runs (e.g. with > mri_concat) and also concatenate the b-value and gradient vector tables > (and make sure the 2 runs are concatenated in the same order for each type > of file!) > > Best, > a.y > > On Fri, 20 May 2016, Kristina Jelinkova wrote: > >> >> Hello all, >> >> >> I had a question regarding the program Tracula. I have two different DTI >> sequences that I wish to run (b=900 and b=2000) but am unsure at which step I >> am suppose to merge the two sequences together. >> >> >> At this point, I have pre-processed each of the sequences separately using >> trac-all. Should I take each of the separate trac-all output >> data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick >> model fit on the new bedpostX output? Also, is there a way to use nii.gz >> files in the configuration file rather than a dcm list? >> >> >> Thank you in advance for your help! >> >> >> > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Mult-Shell Tracula Help
Hi Kristina - I'm assuming the 2 data sets were acquired in the same session and with the same acquisition parameters, other than the b-values? Then you can just concatenate the DWIs from the 2 runs (e.g. with mri_concat) and also concatenate the b-value and gradient vector tables (and make sure the 2 runs are concatenated in the same order for each type of file!) Best, a.y On Fri, 20 May 2016, Kristina Jelinkova wrote: Hello all, I had a question regarding the program Tracula. I have two different DTI sequences that I wish to run (b=900 and b=2000) but am unsure at which step I am suppose to merge the two sequences together. At this point, I have pre-processed each of the sequences separately using trac-all. Should I take each of the separate trac-all output data.nii.gz files, merge them, run bedpostX, and then run the ball-and-stick model fit on the new bedpostX output? Also, is there a way to use nii.gz files in the configuration file rather than a dcm list? Thank you in advance for your help! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Coordinates in TRACULA group analysis
Hi Anri - The FA values are extracted in the native space of each subject, which is why those are the only coordinates that you see. If you want to display the results of your analysis on an average path, after running trac-all -stat, you can use the stats/*.path.mean.txt files (see also the last part of the TRACULA tutorial). Best, a.y On Wed, 18 May 2016, Anri WATANABE wrote: Dear experts, I use TRACULA to examine a measure (FA) at each voxel in one pathway. pathstats.byvoxel.txt files show coordinates in native space and after converting those the new files don't show any coordinates which are in MNI space. Could you tell me how can I know MNI coordinate values? Thank you! Regards, Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] trac-all problem
Hi Qi - Is /Studies/*/DTI/dmrirc_subject a single file or multiple files? What are the contents of that file? a.y On Fri, 6 May 2016, Zeng, Qi wrote: Hi, I am running dti data with trac-all. I followed the command: trac-all -prep -c /Studies/*/DTI/dmrirc_subject but it exited with error "Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension." Before. there is another post about similar problem https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027802.html Dr. Yendiki suggested it could be because missing defined B0 in the dmrirc, but new version wouldn't need this (5.3, a new version?). If so, where can I obtain the B0 data? Can I compute from DICOM like nifti and bval, bvec? Best, Qi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: trac-all -path error
Hi Elijah - Since the error occurs in the CST, is any of the brainstem cut off for this subject? It's hard to tell from the screenshot, but the field of view seems a bit cropped inferiorly. Best, a.y On Thu, 5 May 2016, Elijah Mak wrote: > Dear Anastasia Yendiki, > I ran into a hitch while running trac-all -path and came across an identical > problem where there was a segmentation fault. I have attached my error and > log files. > > Loading initial proposal SD's from > /subject/dlabel/diff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt > > Processing pathway 2 of 18... > > Initializing MCMC > > I have also checked the aparc+aseg and aparc+aseg_mask (overlaid on FA; > screenshot attached) as you have suggested, but I can't seem to find anything > that would have compromised the -path process. > > What else could have gone wrong? trac-all -path works for other subjects. > > Thanks for your help. > > Best Wishes, > Elijah > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Inquiry a single curve problem for Tracula outputs
Hi Xiaofu - It's hard to tell but it looks like the brain mask (which comes from the structural data) is a bit too large in the temporal lobe, so it's possible that the structural-to-diffusion registration didn't go so well for this subject. You can check on this by overlaying the structural segmentation transformed into diffusion space (from dlabel/diff/aparc+aseg...) onto the FA map. Best, a.y On Sun, 1 May 2016, Xiaofu wrote: Dear Anastasia or Tracula-group, I have run Tracula and found there was only one single curve for some tracts. But others went well. I tried setting reinit parameter to 1 and rerunning "trac-all -prior" and "trac-all -path" but didn't get improved, e.g., the right UNC was a single curve (see attached). I also checked the two end point set of right UNC (i.e.,endpt1.pd.nii.gz and endpt2.pd.nii.gz) (see attached) and found those end points were visually not correct when loaded to FA image. I guess that may be the reason of the single curve problem. Is there anyway to fix this problem? Moreover, do you have any suggestions on the tract statistics for those single curve tracts. I'd appreciate it if could take a look at it for me. If you need more files for the diagnosis please let me know. Looking forward to hearing from you. Thank you very much. Best, Xiaofu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula Pathway reconstruction
Hi Peggy - If it looks like a single path, it definitely is an initialization error. If you reinitialize repeatedly and it doesn't get fixed, it might be that something went wrong earlier in the processing (for example some part of brain that the tract goes through is missing from the brain mask). Best, a.y On Mon, 25 Apr 2016, Peggy Skelly wrote: Hi Tracula Experts, How do you determine if a pathway reconstructed well? I've been examining the merged pathways (/dpath/merged_avg33_mni_bbr.mgz) in freeview, and if the pathway looked too small when viewing with the default threshold, I would reinitialize those pathways. Most of the time, the new pathway would look ok upon re-inspection. A few pathways, however, still appear too small when viewed at the default threshold in Freeview, but at lower thresholds, they begin to look ok. I've encountered 1 pathway that still appears too small in Freeview, but the output in pathstats.overall.txt and pathstats.byvoxel.txt seem reasonable. On the other hand, its path distribution (path.pd.nii.gz) does not look like a distribution, but a single path -- there are a 38 voxels with values of 4000, and all others are 0. This doesn't seem right. What could cause this to happen? What objective measure can I use to determine if a pathway is reconstructed well enough? Thanks, Peggy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] bvals bvecs Error
Hi Marissa - If your bvecs/bvals files are in row format, you need to make sure that you have the most recent update that supports this. It was a feature that was added later on: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates Best, a.y On Fri, 15 Apr 2016, Marissa Pifer wrote: Hi freesurfers, I'm having a problem the bvals and bvecs for one of my subject's DTI data. When I try to run the first step of tracula I get this error message: "Error: data and bvals/bvecs do not contain the same number of entries" I have checked, the bvals and bvecs do contain the same amount of entries (42), and they are in the proper format (bvals one line, bvecs three lines). The entries in the bvals/bvecs matches the number of images within the DTI file as well. Looking online, I saw that this was part of the FAQs on tracula. It suggested making sure the locale settings were correct, which it is (en_US.UTF-8). I've run tracula on every other subject and have not run into this problem, but the same subject had an error with multiple frames when we were processing the T2 images. Could this be related? Any idea about what is going on, or how I can fix it? Thanks in advance, Marissa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] REPOST: TRACULA dev version: Error message
Hi Elijah - Are the bvec/bval files located in the current directory from where you are running trac-all? This is where it seems to be looking for them: cp 16084.bvec /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvecs cp 16084.bval /Users/MacPro/Documents/NIMROD_DTI/FS6_16084_MPRAGE_Neuro.nii/dmri/dwi_orig.mghdti.bvals If they're in a different location, you need to specify the full path to that location, as shown in the sample configuration file. Best, a.y On Fri, 15 Apr 2016, Elijah Mak wrote: Hi Freesurfer, Sorry about reposting this email from earlier: I can't seem to get the TRACULA in the dev version of FS6 to run. mv -f /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs mv: rename /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs to /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs: No such file or directory The contents of that folder are: dwi_orig.mghdti.bvals dwi_orig.mghdti.bvecs dwi_orig.nii.gz dwi_orig_flip.nii.gz xfms The full error message is enclosed with this email. Thanks! Best Wishes, Elijah ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] dt_recon image inputs -i flag
Hi Bryan - It'll convert whatever input you give it to nifti, so it's fine if your input is already nifti. Best, a.y On Wed, 6 Apr 2016, Chiu, Bryan (PHTH) wrote: Hi, I’m looking to do some DTI analysis with dt_recon. I have Philips acquired DTI images in par/rec. I ran dcm2nii and have retrieved the associated *bval, *bvec and *nii.gz files that come out. In the tutorial it mentions the -i flag requiring a dcm image. Is it possible to pass a *.nii.gz file ? Regards, ___ Bryan Chiu Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula problems (creating symbolic link)
Hi Efrat - You could just use cp instead of ln -s. This will duplicate the file, instead of creating a link to it. a.y On Tue, 5 Apr 2016, Efrat Kliper wrote: Dear Anastasia, Thank you for the fast replay. I have tried both suggestions, however it still reports: Operation not supported Also, I have used the links that you have sent me but non work. This time (after changing according to the links), I got the message: operation denied I don’t know how to resolve the issue of virtual machine, as not much is written about that and the links are not helping with that issue. Do you have other suggestions regarding how to change the script, so it will create the data.nii without the symbolic link (there are plenty "ln" commands uses in the script)? Many thanks, Efrat On Wed, Mar 30, 2016 at 12:39 AM, Anastasia Yendiki wrote: Hi Efrat - This appears to be a virtual machine problem: https://communities.vmware.com/thread/312591?tstart=0 There are some solutions suggested in that thread. I'm wondering if using a relative instead of an absolute path for the symlink works, i.e., ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz instead of: ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz Can you please try it both ways and let me know if the former works on a computer where the latter doesn't? And yes, if you fix error #1 it'll fix error #2 as well. Thanks, a.y On Tue, 29 Mar 2016, Efrat Kliper wrote: Dear Freesurfer experts, I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has already been completed in Freesurfer 5.1) in order to run some new functions of Tracula (I have also installed the latest Tracula update (tracula.update.centos4_x86_64.5.3.2014_05_26). I am using: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 I encountered two problems: 1. When I run the initial code of Tracula: trac-all –prep code: /home/fsl/ usr/local/freesurfer/bin/trac-all -prep -c /mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt Subject TB_480 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux I am getting the following message: ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz ln: creating symbolic link `/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to `/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not supported 2. If I run the trac-all –bedp command of Tracula (on already trac-all data which was preproc on Freesurfer version 5.1. /home/fsl /usr/local/freesurfer/bin/trac-all -bedp -c /home/fsl/Desktop/xxx.txt Subject TB_201 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux I am getting the following message: Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15
Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction
Hi Emad - I believe that it's not finding your freesurfer recons. They should be under the $SUBJECTS_DIR and have the same names for time points and longitudinal template as what is under your tracula output directory (if the latter is different from SUBJECTS_DIR). Best, a.y On Fri, 1 Apr 2016, Emad Ahmadi wrote: Hi Anastasia, I’ve attached the log files. The cases are: 1. Case #2; time points: 2a, 2b; base template: 2tem 2. Case #3; time points: 3a, 3b; base template: 3tem Thank you again for your help, Emad Emad Ahmadi, MD --- Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu On Apr 1, 2016, at 10:49 AM, Anastasia Yendiki wrote: Hi Emad - The error happens at the very beginning, so I'm wondering if something went wrong in the previous steps, before -path. Can you please send me the entire trac-all.log of one of your subjects? Thank you! a.y On Wed, 30 Mar 2016, Emad Ahmadi wrote: Hi Anastasia, I hope you’re enjoying your evening! I’m doing longitudinal TRACULA analysis on two subjects, each having two time points. I have already taken the steps of longitudinal recon-all and trac-all -prep & -bedp. Now I’m trying to do trac-all -path, but it gives me an error that I cannot recognize. I would greatly appreciate your help. I’ve attached the log files and the config file. Thank you so much, Emad Emad Ahmadi, MD --- Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction
Hi Emad - The error happens at the very beginning, so I'm wondering if something went wrong in the previous steps, before -path. Can you please send me the entire trac-all.log of one of your subjects? Thank you! a.y On Wed, 30 Mar 2016, Emad Ahmadi wrote: Hi Anastasia, I hope you’re enjoying your evening! I’m doing longitudinal TRACULA analysis on two subjects, each having two time points. I have already taken the steps of longitudinal recon-all and trac-all -prep & -bedp. Now I’m trying to do trac-all -path, but it gives me an error that I cannot recognize. I would greatly appreciate your help. I’ve attached the log files and the config file. Thank you so much, Emad Emad Ahmadi, MD --- Research Fellow in Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: e...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula problems (creating symbolic link)
Hi Efrat - This appears to be a virtual machine problem: https://communities.vmware.com/thread/312591?tstart=0 There are some solutions suggested in that thread. I'm wondering if using a relative instead of an absolute path for the symlink works, i.e., ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz instead of: ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz Can you please try it both ways and let me know if the former works on a computer where the latter doesn't? And yes, if you fix error #1 it'll fix error #2 as well. Thanks, a.y On Tue, 29 Mar 2016, Efrat Kliper wrote: Dear Freesurfer experts, I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has already been completed in Freesurfer 5.1) in order to run some new functions of Tracula (I have also installed the latest Tracula update (tracula.update.centos4_x86_64.5.3.2014_05_26). I am using: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 I encountered two problems: 1. When I run the initial code of Tracula: trac-all –prep code: /home/fsl/ usr/local/freesurfer/bin/trac-all -prep -c /mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt Subject TB_480 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux I am getting the following message: ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz ln: creating symbolic link `/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to `/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not supported 2. If I run the trac-all –bedp command of Tracula (on already trac-all data which was preproc on Freesurfer version 5.1. /home/fsl /usr/local/freesurfer/bin/trac-all -bedp -c /home/fsl/Desktop/xxx.txt Subject TB_201 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux I am getting the following message: Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May
Re: [Freesurfer] FA and MD *positively* correlated within same regions ?
Hi Elijah - I suggest looking at the axial diffusivity (AD) and radial diffusivity (RD) to help you interpret these results. These are the diffusivity parallel and perpendicular to the main budnle going through a voxel, respectively. Essentially, FA tells you how different the AD and RD are from each other, and MD tells you how big AD and RD are in aggregate. Here are just a couple of all the possible scenarios that can lead to opposite FA/MD relationships: AD increases, RD stays the same => MD increases, FA increases AD stays the same, RD increases => MD increases, FA decreases Hope this helps, a.y On Thu, 24 Mar 2016, Elijah Mak wrote: Hi Freesurfer Community, I recently used mri_segstats to extract FA and MD as suggested here: http://freesurfer.net/fswiki/FsTutorial/Diffusion Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at some of the correlations between FA and MD in the same regions, and came across a few interesting ones. wm_lh_entorhinal FA & wm_lh_entorhinal MD: r = 0.6, p <0.001 ctx_lh_entorhinal FA & ctx_lh_entorhinal MD: r = -0.3, p < 0.020 wm_lh_precuneus FA & wm_lh_precuneus MD: r = -0.6, p <0.001 As I understand, a clear-cut interpretation especially with regards to FA changes is not so easy! But could someone discuss / speculate as to why FA and MD could be positively correlated within the entorhinal WM region? That was found separately within a group of a elderly healthy controls and a group of dementia subjects. Thank you for your time! Best Wishes, Elijah ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Trac-all -path Segmentation error
Hi Katherine - The dlabel/ directory is created during the -prep step, when the structural segmentation gets mapped from T1 to diffusion space. However bedpost may still run fine without the dlabel/ directory. It seems that the problem is fairly early in the -prep step. Any errors there? Best, a.y On Wed, 23 Mar 2016, Katherine Damme wrote: Hey Anastasia, Although the bedpost appears to complete properly the dlabel/diff is not being created during the bedp step. I am not sure how or why this error is occurring. That would, it appears, definitely be the cause of the failure. However, I am not getting an error during the prep or the bedpost stage, and so I am still completely lost any advice would be deeply appreciated! Thank you, KD On Wed, Jan 13, 2016 at 6:07 PM, Anastasia Yendiki wrote: Hi Katherine - Do the freesurfer segmentations look ok? What about the registration from structural to diffusion? You can inspect those quickly with: freeview dmri/dtifit_FA.nii.gz dlabel/diff/aparc+aseg.bbr.nii.gz:colormap=lut:opacity=.3 Hope this helps, a.y On Sun, 3 Jan 2016, Katherine Damme wrote: First I should note that using the same scripts I completed 52 participants successfully and am currently trying to batch process the newest 42 participants that are only failing at the path level. Upon Visual Inspection they all appear normal (with the exception of the one attached). After carefully comparing a random sample of 5 from each group images from the files that failed versus the files that were successful, I found: 1. The range of values in the mean_ph1samples in the successful ( i.e. -3.00 to 87.30 ) differed from the failures (i.e. -2 to 17) (the successful samples varied on their high end from 50-114 but the failures were on the 5-24 range) 2. The range of values in the mean_th1samples in the successful ( -0.02 to 19.12) differed from the failures (-0.00267 to 7.176) (the successful samples varied on their high end from 19-17 but the failures were on the 3-10 range) 3. Some, but not all (2/5), mean_S0samples, had a abnormal range in successful (0 to 19998.4) compared to the unsuccessful (0 to 709.96) However, I understand that the diffusion units are likely arbitrary and not sure these patterns will hold in a larger sample. I know this is a lot of confusing information and so in response to your question. After an initial inspection there are two types of output: 1. data that appears visually normal with a slightly altered range. Should I be concerned about the range if all other data looks fine? 2. data that appears visually normal with a normal range and bizarre merged files. What do you think could be a cause of these odd merged files? On Tue, Dec 22, 2015 at 1:54 PM, Anastasia Yendiki wrote: Hi Katherine - Have you looked at any of the intermediate images? Do they look normal? a.y On Mon, 21 Dec 2015, Katherine Damme wrote: Hello Everyone! It looks as though my prep and bedp stages completed properly, but the prep stage ends in a segmentation errror. See attached and let me know your thoughts. I would prefer not to have to redo all steps if possible! Thank you! The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners
Re: [Freesurfer] Tracula bedpostx error
Hi Prad - I'm guessing the tutorial was generated with an earlier version of bedpostx, tracula, or a combination of both. So I wouldn't expect to find the exact same values. As long as things run and the files are generated, it looks like you're fine. Best, a.y On Mon, 7 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote: > Hi Anastasia, > > Thank you for clarifying that. I have a follow up question. > > To avoid this error while running the ball and stick model fit( Syntax error: > "(" unexpected), I ran it locally using "bedpostx $path_to_dmri". > > The results of the overall path statistics differ from those in the tutorial. > I've attached my results for the left ILF (pathstats.overall_redone.txt) and > the tutorial results (pathstats.overall_original.txt) > > Is this difference due to running them on different machines or is because I > had to run the bedpostx command directly ? > > Thanks! > -Prad > _______ > > _ > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Anastasia Yendiki > > Sent: Monday, March 7, 2016 10:19 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] Tracula bedpostx error > > Hi Prad - What will affect the speed is whether you run it locally on your > computer (in which case it'll process one slice after the other) or on a > cluster (in which case all the slices will be processed in parallel on > different nodes of the cluster). This is the case regardless of the > version that you use. > > Best, > > a.y > > On Sun, 6 Mar 2016, Bharadwaj, Pradyumna - (prad) wrote: > >> >> >> Hello Anastasia, >> >> I have been trying to run through the tutorial with one of the subjects from >> the tutorial(elmo.2008) to familiarize myself with Tracula. >> The preprocessing step seems to have been completed without any errors (Log >> file attached).However, when I proceed with the ball and stick model fit >> step, I get the following error >> >> bedpostx_mgh -n 2 /home/biba1/testing_tracula/diffusion/elmo.2008/dmri >> /apps/freesurfer/bin/bedpostx_mgh: 131: /apps/freesurfer/bin/bedpostx_mgh: >> Syntax error: "(" unexpected. I'm running the tutorial locally on Ubuntu >> 12.04 with FSL 5.0.9. >> >> In an earlier post where the same error was >> encountered(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg38004.html) >> you recommended >> running bedpostx directly. >> >> Would this impact the results or run time in any way? and is there something >> I can do to fix this error if it is likely to take much longer? >> >> >> Thanks! >> >> -Prad >> >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] path.pd.trk format
Anatorig will take you to freesurfer space. I's suggest smoothing these to make them more presentable, and potentially also thresholding them based on the probability map (which is the sum of these streamlines). On Mon, 7 Mar 2016, Peled, Noam wrote: > I want to display it in my new 3d visualization tool, along the hemispheres > and the subcortical regions. > The hemispheres and the subcortical regions I import from freesurfer. > > Thanks, > Noam > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Monday, March 07, 2016 12:20 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] path.pd.trk format > > What to you want to display it on? If you want to display in on the FA > map, or anything that's in diffusion space, you don't need any transform. > > On Mon, 7 Mar 2016, Peled, Noam wrote: > >> So for plotting the fibers, like in freeview, should I just use the >> /dmri/xfms/diff2anatorig..mat or >> /dmri/xfms/diff2anat..mat transformation matrices? >> >> Thanks again, >> Noam >> ____ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Monday, March 07, 2016 12:09 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] path.pd.trk format >> >> Yes, native diffusion space. >> >> On Mon, 7 Mar 2016, Peled, Noam wrote: >> >>> Thanks! >>> Do you in which space are the voxel coordinates coordinates? Are they in >>> the diffusion space? >>> >>> Thanks again, >>> Noam >>> >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >>> [ayend...@nmr.mgh.harvard.edu] >>> Sent: Saturday, March 05, 2016 5:10 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] path.pd.trk format >>> >>> Hi Noam - You can read the .trk file with trackvis. It contains all the >>> path samples that are added up to created the probability distribution of >>> the path. Please keep in mind, however, that this .trk file is just meant >>> for generating stats and not for visualization, so these are not the usual >>> smoothed kind of streamlines that you get from deterministic tractography. >>> It contains only integer voxel coordinates, so the streamlines will look >>> sort of like step ladders if you visualize them. >>> >>> Best, >>> >>> a.y >>> >>> On Tue, 16 Feb 2016, Peled, Noam wrote: >>> >>>> Hello, >>>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the >>>> output directory. >>>> How can I read this file? I would like to read the actual splines and not >>>> the probabilistic distribution in path.pd.nii.gz. >>>> >>>> Thanks, >>>> Noam Peled >>>> >>>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] path.pd.trk format
What to you want to display it on? If you want to display in on the FA map, or anything that's in diffusion space, you don't need any transform. On Mon, 7 Mar 2016, Peled, Noam wrote: > So for plotting the fibers, like in freeview, should I just use the > /dmri/xfms/diff2anatorig..mat or > /dmri/xfms/diff2anat..mat transformation matrices? > > Thanks again, > Noam > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki > [ayend...@nmr.mgh.harvard.edu] > Sent: Monday, March 07, 2016 12:09 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] path.pd.trk format > > Yes, native diffusion space. > > On Mon, 7 Mar 2016, Peled, Noam wrote: > >> Thanks! >> Do you in which space are the voxel coordinates coordinates? Are they in the >> diffusion space? >> >> Thanks again, >> Noam >> >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki >> [ayend...@nmr.mgh.harvard.edu] >> Sent: Saturday, March 05, 2016 5:10 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] path.pd.trk format >> >> Hi Noam - You can read the .trk file with trackvis. It contains all the >> path samples that are added up to created the probability distribution of >> the path. Please keep in mind, however, that this .trk file is just meant >> for generating stats and not for visualization, so these are not the usual >> smoothed kind of streamlines that you get from deterministic tractography. >> It contains only integer voxel coordinates, so the streamlines will look >> sort of like step ladders if you visualize them. >> >> Best, >> >> a.y >> >> On Tue, 16 Feb 2016, Peled, Noam wrote: >> >>> Hello, >>> I've noticed that in tracula 5.2 there's also a path.pd.trk file in the >>> output directory. >>> How can I read this file? I would like to read the actual splines and not >>> the probabilistic distribution in path.pd.nii.gz. >>> >>> Thanks, >>> Noam Peled >>> >>> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.