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

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

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

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

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

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/

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

[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

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

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:

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 

Re: [Freesurfer] dmri_poistats

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

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”

Re: [Freesurfer] TRACULA: narrow probability distributions

: 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" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu> wrote: Hi Michael - Even if it starts very c

Re: [Freesurfer] TRACULA: narrow probability distributions

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" <fr

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,

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

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

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

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

Re: [Freesurfer] Projecting FA map onto fsaverge surface

! Best, Taha On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> 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

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

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

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

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

[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

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

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

Re: [Freesurfer] How to run part of TRACULA

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 <ayend...@nmr.mgh.harvard.edu> wrote: Hi Athanasia - TRACULA expects certains files named a certain way to be there at the end of each preproc

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

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

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

Re: [Freesurfer] Coordinates in TRACULA group analysis

** 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: 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

Re: [Freesurfer] Coordinates in TRACULA group analysis

tal, Kyoto Prefectural University of Medicine ** 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic model of

Re: [Freesurfer] Coordinates in TRACULA group analysis

Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: 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 t

Re: [Freesurfer] TRACULA: 20% default threshold

-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu> 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

Re: [Freesurfer] TRACULA fornix tractography

> > 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, Barbar

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

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 >

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:

Re: [Freesurfer] TRACULA group stats visualization

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 &g

Re: [Freesurfer] Coordinates in TRACULA group analysis

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 Yend

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

/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

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

Re: [Freesurfer] Coordinates in TRACULA group analysis

** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ** 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: Hi Anri - Is there an

Re: [Freesurfer] TRACULA tract group comparison p-values

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, > > Bar

Re: [Freesurfer] Fwd: TRACULA stat extraction issue

know. Thanks Shashwath On Mon, Jul 4, 2016 at 3:25 AM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> 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

Re: [Freesurfer] TRACULA group stats visualization

ile 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,

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

Re: [Freesurfer] TRACULA group stats visualization

> -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: F

Re: [Freesurfer] Coordinates in TRACULA group analysis

03 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: 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:

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

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

what this could be ? Thanks, Ismail On Jul 4, 2016, at 3:15 PM, Koubiyr, Ismail <ikoub...@bwh.harvard.edu> 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 Y

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

. Also why the DICOMs wouldn’t work at the beginning ? Thanks, Ismail On Jul 4, 2016, at 2:41 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> wrote: Hi Ismail - You can see from the log file that the command that causes the error is this: mri_convert --frame 31 /Users/ismailk

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

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 <ayend...@nmr.mgh.harvard.edu> wrote: > > > Hi Ismail - It sounds like the error has to do wit

Re: [Freesurfer] [TRACULA] ERROR: cannot unpack mosiacs without ASCII header

ors. 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 <

Re: [Freesurfer] longitudinal tracula

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" <fr

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

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

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

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.

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

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

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

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

Re: [Freesurfer] Coordinates in TRACULA group analysis

** 2016-05-31 22:55 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: 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

Re: [Freesurfer] Tracula skip steps

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" <ayend...@nmr.mgh.harvard.edu> 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 Ma

Re: [Freesurfer] Tracula skip steps

much Heidi On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu> wrote: Hi Heidi - It knows where to find the freesurfer recons of the T1's from SUBJECTS_DIR (se

Re: [Freesurfer] Tracula skip steps

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" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of ayend...@nmr.mgh.harvard.edu> wrote: No, it should be pointed to the DWI data, which can be correcte

Re: [Freesurfer] Tracula skip steps

) 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 Ye

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

Re: [Freesurfer] Coordinates in TRACULA group analysis

Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: 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 tr

Re: [Freesurfer] DTI error

es <jal...@usc.edu> wrote: Correct.  On Sunday, May 22, 2016, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> 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

Re: [Freesurfer] DTI error

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 <ay

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 <ay

Re: [Freesurfer] DTI error

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 <ayend...@nmr.mgh.harvard.edu> wrote: But do you see the output files from the previous step? The outputs from each step are described on the wiki. On Sun,

Re: [Freesurfer] DTI error

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 <ayend...@nmr.mgh.harvard.edu> wrote: Hi Jasmin - Check if things are running despite that error. Are output files

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:

Re: [Freesurfer] Mult-Shell Tracula Help

<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki > <ayend...@nmr.mgh.harvard.edu> > 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 s

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

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

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

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

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

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

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:

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

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

Re: [Freesurfer] Tracula problems (creating symbolic link)

. 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 <ayend...@nmr.mgh.harva

Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction

--- 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 <ayend...@nmr.mgh.harvard.edu> wrote: Hi Emad - The error h

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

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

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

Re: [Freesurfer] Trac-all -path Segmentation error

. 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 <ayend...@nmr.mgh.harvard.edu> wrote: Hi Katherine - Do the free

Re: [Freesurfer] Tracula bedpostx error

hines or is because I > had to run the bedpostx command directly ? > > Thanks! > -Prad > ___ > > _ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki > <aye

Re: [Freesurfer] path.pd.trk format

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 >

Re: [Freesurfer] path.pd.trk format

g..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

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

Re: [Freesurfer] path.pd.trk format

n...@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

Re: [Freesurfer] TRACULA messy tracts

Hi Jacek - I looked at the data that you uploaded. The problem is that both the b-value table and the gradient table that you were using were assuming that the b=0 images were interspersed throughout your scan, when in fact based on your dicoms they are all in the begining of the scan. So

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