Re: [Freesurfer] network analysis in tracula
Hi Amelia - I guess the questions are what would be the end ROIs for a connectivity matrix derived from tracula, and what would be defined as connectivity strength. What's the goal of this analysis? a.y On Fri, 22 May 2015, Versace, Amelia wrote: Dear Anastasia, Is there a way to get connectivity matrices using the outputs of tracula? Thanks a lot, Amelia ___ 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] FW: correcting for brain size
Hi Gabriella, I'm not an expert in freesurfer. I've worked with freesurfer for 5 years now. When we started I had the same problem when including ICV in the qdec table and running it as a nuisance variable. I'm assuming you have ICV in mm^3. Try converting it to cm^3 or dcm^3 in your qdec table. That worked for us. I think qdec might have a problem with numbers in the millions/hundred thousands. Just don't forget to reconvert when you are interpreting/writing your results or else it can get confusing. Maybe its just us, but when we use ICV as a covariate many, many significant clusters were diminished to nothing. Hope this helps. -David Vazquez PhD candidate in Cognitive Neuroscience University of California, Riverside NSF GRFP fellow On Fri, May 22, 2015 at 6:16 AM Hirsch, Gabriella gabriella_hir...@meei.harvard.edu wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella *From:* Hirsch, Gabriella *Sent:* Wednesday, May 20, 2015 3:55 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1. So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? 2. I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? 3. If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. I’d really appreciate any help on this. Thank you! Gabriella ___ 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.
[Freesurfer] network analysis in tracula
Dear Anastasia, Is there a way to get connectivity matrices using the outputs of tracula? Thanks a lot, Amelia ___ 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_SNR
I got it.
Thanks a lot
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Friday, May 22, 2015 3:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
Standard deviation is the variation around the mean. The more the noise, the
more the variation.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
But in our command line
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk
'{print $1/$2}' dwi_snr.txt
the flag -m is the mean intensity and the flag -s is the standard
deviation for the intensity
Here we are using the same mask White-Matter++.flt.nii.gz so the output
is mean intensity for the signal behind this mask and the standard deviation
for the intensity behind this mask.
Why the standard deviation is noise?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia
Yendiki
Sent: Friday, May 22, 2015 3:15 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
The mean is the signal, the standard deviation is the noise.
http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definit
ion
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
I am sure that I am missing something.
Kindly, the purpose of my question is to improve my understanding for this
issue.
SNR is a ratio between signal and noise. Tracula's command line is dividing
the mean intensity for an ROI by the standard deviation for the same ROI so
why the output is ratio between signal and noise? I can't find any
evaluation for the noise in this method.
Looking forward to learn from you
Bests,
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
Anastasia Yendiki
Sent: Friday, May 22, 2015 1:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
There's no perfect way to estimate SNR unfortunately. For example, using the
background outside the brain would mean that you'd be using locations
outside the head coil, and the noise there is not going to be representative
of the noise inside the head coil.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasi,
Thank you very much for your support.
Actually I did. I checked trac-all.log and I found the following command
line:
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk
'{print $1/$2}' dwi_snr.txt
Here is the reason for my question:
I know that the SNR can be calculated by the ratio of ( the mean
intensity in a WM area like the corpus callosum (for example) and
the standard deviation (or the mean) for a region in the background
outside the brain that does not contain any artefacts. Then we can
add some kind of correction factors to account for the fact that the
noise distribution is not Gaussian
(http://www.ncbi.nlm.nih.gov/pubmed/17622966)
What I noticed in Tracula's command line that it calculate the SNR by
dividing the mean and the standard deviation for an area behind the mask.
That's why I am confused.
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
Anastasia Yendiki
Sent: Friday, May 22, 2015 11:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
Hi Mohamad - You can search for dwi_snr in the trac-all.log file to see
the command line that produces this file.
a.y
On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
“dwi_snr.txt” is an output of the preprocessing step in TRACULA.
Kindly how TRACULA is calculating the SNR for every direction in DTI data?
Is there any command line that can do it?
Thanks,
Mohamad
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[Freesurfer] Fwd: recon-all issue
Hello, So recon-all seems to be running on my Mac fine, with this same data. But it does not run on my institution's Minerva linux server. It did most of volumetric processing steps, but failed on surface processing steps, and then all of the rest. I have checked that environment variables are correct, and they are I believe. Attached is the entire recon-all.log file I will appreciate any help! Thank you very much, Anvi recon-all.log Description: Binary data ___ 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] mni305 volume-based analysis
Hi list, I'm configuring mkanalysis-sess to configure an analysis for FC data by FS-FAST. I do not understand how I can perform mni305 volume-based analysis. How can I configure an analysis for mni305? Specifically, which is the paradigm file in -taskreg? How is the command for group level preprocessing using seg305? I have performed these step: 1. Analyze anatomicals in FreeSurfer (recon-all) 2. Create subjectname file. 3. Preprocessing preproc-sess -s Sess01 -fwhm 5 -surface fsaverage lhrh -mni305 -fsd rest -per-run 4. Parameters configuration to creates a text file describing the FC seed for an individual. fcseed-config -segid 10 -fcname L_Thalamus.dat -fsd rest -mean -cfg mean.L_Thalamus.config fcseed-config -segid 49 -fcname R_Thalamus.dat -fsd rest -mean -cfg mean.R_Thalamus.config 5. fcseed-sess -s Sessid -cfg mean.R_Thalamus.configfcseed-sess -s Sessid -cfg mean.L_Thalamus.config 6. Create nuisance variables: fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config fcseed-sess -s sessionid -cfg wm.config fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config fcseed-sess -s sessionid -cfg vcsf.config 7. selxavg3-sess -s Sessid -a fc.lthalseed.surf.lhselxavg3-sess -s Sessid -a fc.rthalseed.surf.lh ThanksStefano ___ 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] Hippocamp subfields
yes, but the ones in V6 (which someday will make it out) are more accurate. You can get a beta and try them out if you want. cheers Bruce On Fri, 22 May 2015, Hassan bakhshi wrote: Hi, I am using freesurfer v5.3, can I have hippocamp subfields in this version?? Kind regards ___ 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] FW: correcting for brain size
HI FS experts, I haven't heard back and am still wrestling with these questions. Any takers? I'd really appreciate any thoughts at all if possible. Thanks, Gabriella From: Hirsch, Gabriella Sent: Wednesday, May 20, 2015 3:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1. So far, I've been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to mean center the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? 2. I've found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating - is there any way around this issue? 3. If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what's the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I'm executing this correctly. I'd really appreciate any help on this. Thank you! Gabriella ___ 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_SNR
Hi Mohamad - You can search for dwi_snr in the trac-all.log file to see the command line that produces this file. a.y On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote: Hi Anastasia, “dwi_snr.txt” is an output of the preprocessing step in TRACULA. Kindly how TRACULA is calculating the SNR for every direction in DTI data? Is there any command line that can do it? Thanks, 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 results / pathstats.overall.txt
Hi Michelle - If you want to regenerate the stats with a different threshold for a specific tract, you can run the dmri_pathstats command and use the --pthr option with something other than the default 0.2. You can search your trac-all.log file to see the dmri_pathstats command line that's run by default and modify it. Running it without any arguments will show you a short explanation of the options. Best, a.y On Thu, 19 Mar 2015, Michele Cavallari wrote: Hi there,I have a couple questions regarding TRACULA results. When I visualize the probability distributions of all white-matter pathways simultaneously in some cases the tracts are very small, but by adjusting the threshold I am able to visualize the tract in its entire (and expected) path. So, question#1: The results included in the pathstats.overall.txt file are produced using the default threshold? It looks like the Volume is very small in those tracts that I can visualize only by playing with the threshold. I was wondering whether the DTI metrics can be also impacted. Which leads me to question#2: Do I need to re-run the whole processing (e.g. with -prior option) to get more accurate fiber tracking and DTI results, or there is a way I can adjust the threshold for computation of the DTI (and other) results? Thank you, -Michele ___ 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] tksurfer crash when loading surfaces
Hi Jesse the thickness files are scalar fields over the surface, not surfaces themselves. Load it as an overlay, not as a surface cheers Bruce On Fri, 22 May 2015, Jesse Bledsoe wrote: Hi everyone, I searched the wiki and old posts but couldn't find a solution to this issue. I had no problems with the full recon-all script though got hung up trying to load surfaces in tksurfer. The surface files are there but the buttons in tksurfer aren't bright so I tried to load them manually which causes a crash. Build stamp is below. #@#%# recon-all-run-time-hours 7.729 recon-all -s Epi001 finished without error at Thu May 21 21:15:58 PDT 2015 done (Looks like recon-all finished without error, though quickly, only 7 hours) Then I wanted to look at the surface overlays: bledsoe1 @ivan:~/Desktop/Epilepsy$ tksurfer Epi001 rh inflated Xlib: extension NV-GLX missing on display :2002.0. subject is Epi001 hemi is rh surface is inflated surfer: current subjects dir: /var/local/scratch/bledsoe1/Desktop/Epilepsy/ surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /var/local/scratch/bledsoe1/Desktop/Epilepsy checking for nofix files in 'inflated' Reading image info (/var/local/scratch/bledsoe1/Desktop/Epilepsy//Epi001) Reading /var/local/scratch/bledsoe1/Desktop/Epilepsy//Epi001/mri/orig.mgz surfer: Reading header info from /var/local/scratch/bledsoe1/Desktop/Epilepsy//Epi001/mri/orig.mgz surfer: vertices=134040, faces=268076 surfer: single buffered window surfer: tkoInitWindow(Epi001) Xlib: extension NV-GLX missing on display :2002.0. surfer: using interface /usr/local/freesurfer/stable5_3/tktools/tksurfer.tcl Reading /usr/local/freesurfer/stable5_3/tktools/tkm_common.tcl Reading /usr/local/freesurfer/stable5_3/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/stable5_3/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/stable5_3/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % surfer: loaded pial into set 3 nquads=12582916, nvertices=528 ERROR: MRISread: file '/var/local/scratch/bledsoe1/Desktop/Epilepsy/Epi001/surf/lh.thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! I've done a lot of reconstructions on different data (this is a new data set) and never seen this problem. Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_3 FSFAST_HOME /usr/local/freesurfer/stable5_3/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /var/local/scratch/bledsoe1/Desktop/Epilepsy/ MNI_DIR /usr/local/freesurfer/stable5_3/mni FSL_DIR /usr/share/fsl/5.0 Thank you, Jesse Bledsoe ___ 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 related to bvec/bval input
Hi Scott - The gradient table produced by dcm2nii is formatted in 3 rows, rather than 3 columns. If you want to use gradient tables formatted in rows, you have to download the tracula update described here: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates a.y On Tue, 7 Apr 2015, Scott Quadrelli wrote: Hi, I am trying to get TRACULA running. I have converted the DTI data using dcm2nii (as i was unable to get tracula to read the .ima Siemens DICOM) and have a bevc and bval file output from dcm2nii. The error I get is in bold below (from trac-all.log). I believe that the error is coming from the bevy/bval file however I can’t see what the issue is with the data contained within the file. Does the output from dcm2nii need to be reformatted for input to TRACULA ? Cheers, Scott - /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Tue 7 Apr 2015 21:43:25 AEST mri_convert /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/JA_firstexp.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz mri_convert /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/JA_firstexp.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/JA_firstexp.nii.gz... TR=9000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.99802, 0.0188805, 0.0599977) j_ras = (0.0278771, 0.987856, 0.152851) k_ras = (0.0563831, -0.154221, 0.986426) writing to /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz... cp /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/bvec.txt /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvecs cp /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_analysis/first_exp/bval.txt /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvals flip4fsl /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -9.38889 fslswapdim /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.nii.gz x y z /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz INFO: found /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.mghdti.bvecs /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/bvecs mv -f /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.mghdti.bvals /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/bvals mv -f /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_orig_flip.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi.nii.gz ln -sf /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi.nii.gz /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/data.nii.gz mri_concat --i /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_frame.nii.gz --mean --o /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/lowb.nii.gz niiRead(): error opening file /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_frame.nii.gz ninputs = 1 Checking inputs ERROR: reading /Users/quadrellis/MultiBand_DTI/DTI_processing/JA/DTI_tracula/JA/dmri/dwi_frame.nii.gz Darwin Scotts-MacBook-Pro.local 14.1.0 Darwin Kernel Version 14.1.0: Thu Feb 26 19:26:47 PST 2015; root:xnu-2782.10.73~1/RELEASE_X86_64 x86_64 ___ 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] freesurfer-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)
Hi I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I start mri_convert on ubuntu 14.04.4 I get this results. knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME= /usr/local/freesurfer60 knutjb@dmed4960:/usr/local/freesurfer60$ source /usr/local/freesurfer60/SetUpFreeSurfer.sh freesurfer-Linux-centos7_x86_64-dev-20150521 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer60 FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/knutjb/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 knutjb@dmed4960:/usr/local/freesurfer60$ mri_con mri_concatmri_concatenate_lta mri_convert_crash mri_concatenate_gcam mri_convert mri_convert_mdh knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert --help Illegal instruction (core dumped) knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert -h Illegal instruction (core dumped) knutjb@dmed4960:/usr/local/freesurfer60$ and in GDB Starting program: /usr/local/freesurfer60/bin/mri_convert [Thread debugging using libthread_db enabled] Using host libthread_db library /lib/x86_64-linux-gnu/libthread_db.so.1. Program received signal SIGILL, Illegal instruction. 0x006be48f in make_cmd_version_string (argc=argc@entry=1, argv=argv@entry=0x7fffdd98, id_string=id_string@entry=0xc6de08 $Id: mri_convert.c,v 1.221 2015/04/16 18:56:00 greve Exp $, version_string=version_string@entry=0xc6cd66 $Name: $, return_string=return_string@entry=0x7fffb0e0 (\rW\366\377\177) at version.c:215 215version.c: No such file or directory. Knut Jørgen Bjuland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)
That particular developmental build is compiled with optimization flags for machines containing Intels new Haswell processor and wont run on platforms without it. Although that build is available via our dev download page, it remains an unsupported build that exists primarily for internal experimental purposes only. -Zeke On 05/22/2015 11:49 AM, Knut J Bjuland wrote: Hi I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I start mri_convert on ubuntu 14.04.4 I get this results. knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME= /usr/local/freesurfer60 knutjb@dmed4960:/usr/local/freesurfer60$ source /usr/local/freesurfer60/SetUpFreeSurfer.sh freesurfer-Linux-centos7_x86_64-dev-20150521 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer60 FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/knutjb/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 knutjb@dmed4960:/usr/local/freesurfer60$ mri_con mri_concatmri_concatenate_lta mri_convert_crash mri_concatenate_gcam mri_convert mri_convert_mdh knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert --help Illegal instruction (core dumped) knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert -h Illegal instruction (core dumped) knutjb@dmed4960:/usr/local/freesurfer60$ and in GDB Starting program: /usr/local/freesurfer60/bin/mri_convert [Thread debugging using libthread_db enabled] Using host libthread_db library /lib/x86_64-linux-gnu/libthread_db.so.1. Program received signal SIGILL, Illegal instruction. 0x006be48f in make_cmd_version_string (argc=argc@entry=1, argv=argv@entry=0x7fffdd98, id_string=id_string@entry=0xc6de08 $Id: mri_convert.c,v 1.221 2015/04/16 18:56:00 greve Exp $, version_string=version_string@entry=0xc6cd66 $Name: $, return_string=return_string@entry=0x7fffb0e0 (\rW\366\377\177) at version.c:215 215version.c: No such file or directory. Knut Jørgen Bjuland ___ 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: cannot open file `1000' for reading Bedpost file error
Hi Katherine - Is your gradient table in 3-row format by any chance? This only works with the tracula update that was posted after the freesurfer 5.3 release. If you reinstalled freesurfer (as you mentioned earlier) you might have overwritten the update, in which case the row-formatted gradient table wouldn't work any more. http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates a.y On Mon, 30 Mar 2015, Katherine Damme wrote: Hello Anastasia, I did specify the files. I used the same config file (attached) a few months ago to write make a tracula image and then the dpath was deleted by mistake and when I tried to rerun the same file it is giving me this error. On Fri, Mar 6, 2015 at 6:07 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Katherine - Did you specify the gradient table and b-value table in your configuration file? I suspect that the issue is that it can't find them. a.y On Tue, 3 Mar 2015, Katherine Damme wrote: Hello Freesurfers, I recently updated my Freesurfer version and now I am getting an error in tracula. awk: cmd. line:1: fatal: cannot open file `1000' for reading (No such file or directory) Any help would be appreciated. ___ 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_SNR
Hi Anastasi,
Thank you very much for your support.
Actually I did. I checked trac-all.log and I found the following command line:
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}'
dwi_snr.txt
Here is the reason for my question:
I know that the SNR can be calculated by the ratio of ( the mean intensity in a
WM area like the corpus callosum (for example) and the standard deviation (or
the mean) for a region in the background outside the brain that does not
contain any artefacts. Then we can add some kind of correction factors to
account for the fact that the noise distribution is not Gaussian
(http://www.ncbi.nlm.nih.gov/pubmed/17622966)
What I noticed in Tracula's command line that it calculate the SNR by dividing
the mean and the standard deviation for an area behind the mask.
That's why I am confused.
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Friday, May 22, 2015 11:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
Hi Mohamad - You can search for dwi_snr in the trac-all.log file to see the
command line that produces this file.
a.y
On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
“dwi_snr.txt” is an output of the preprocessing step in TRACULA.
Kindly how TRACULA is calculating the SNR for every direction in DTI data? Is
there any command line that can do it?
Thanks,
Mohamad
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Re: [Freesurfer] TRACULA NIFTI Images
Hi Lucas - Only if you had DICOM files, you'd be able to specify one of the dicom files and it would find the rest if they're all in the same directory. But if you have any other format (NIfTI in your case), then all the volumes from a subject's diffusion scan should in one file. I you have volumes as separate files, you can put them all together into one file with mri_concat. Make sure that the order in which they are merged into this file is the same order as the corresponding b-values and gradient vectors are listed in your b-value table and gradient table. Best, a.y On Tue, 31 Mar 2015, Lucas Lessa wrote: Dear Colleagues, I'm having problem to process TRACULA. I already processed the T1 imagens (recon-all) but I can't go further with the DWI imagens. I think that the problem is my image type. I have 33 files (1 b0 and 32 different directions) and in the configuration file I pointed to the first image (b0). Tracula starts the first step (-prep) but hangs after 1h. Do you think I need to convert the images or do I need to use a 4D NIFTI file? Last but not least, I have to say that I don't have the DICOM files, just PAR/REC. Thank you. Lucas Lessa. ___ 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] tksurfer crash when loading surfaces
Hi everyone, I searched the wiki and old posts but couldn't find a solution to this issue. I had no problems with the full recon-all script though got hung up trying to load surfaces in tksurfer. The surface files are there but the buttons in tksurfer aren't bright so I tried to load them manually which causes a crash. Build stamp is below. #@#%# recon-all-run-time-hours 7.729 recon-all -s Epi001 finished without error at Thu May 21 21:15:58 PDT 2015 done *(Looks like recon-all finished without error, though quickly, only 7 hours)* *Then I wanted to look at the surface overlays:* bledsoe1 @ivan:~/Desktop/Epilepsy$ tksurfer Epi001 rh inflated Xlib: extension NV-GLX missing on display :2002.0. subject is Epi001 hemiis rh surface is inflated surfer: current subjects dir: /var/local/scratch/bledsoe1/Desktop/Epilepsy/ surfer: not in scripts dir == using cwd for session root surfer: session root data dir ($session) set to: surfer: /var/local/scratch/bledsoe1/Desktop/Epilepsy checking for nofix files in 'inflated' Reading image info (/var/local/scratch/bledsoe1/Desktop/Epilepsy//Epi001) Reading /var/local/scratch/bledsoe1/Desktop/Epilepsy//Epi001/mri/orig.mgz surfer: Reading header info from /var/local/scratch/bledsoe1/Desktop/Epilepsy//Epi001/mri/orig.mgz surfer: vertices=134040, faces=268076 surfer: single buffered window surfer: tkoInitWindow(Epi001) Xlib: extension NV-GLX missing on display :2002.0. surfer: using interface /usr/local/freesurfer/stable5_3/tktools/tksurfer.tcl Reading /usr/local/freesurfer/stable5_3/tktools/tkm_common.tcl Reading /usr/local/freesurfer/stable5_3/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/stable5_3/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/stable5_3/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % surfer: loaded pial into set 3 nquads=12582916, nvertices=528 ERROR: MRISread: file '/var/local/scratch/bledsoe1/Desktop/Epilepsy/Epi001/surf/lh.thickness' has many more faces than vertices! Probably trying to use a scalar data file as a surface! I've done a lot of reconstructions on different data (this is a new data set) and never seen this problem. *Build stamp:* freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable5_3 FSFAST_HOME /usr/local/freesurfer/stable5_3/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /var/local/scratch/bledsoe1/Desktop/Epilepsy/ MNI_DIR /usr/local/freesurfer/stable5_3/mni FSL_DIR /usr/share/fsl/5.0 Thank you, Jesse Bledsoe ___ 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: drmirc parameteres with already processed and registered data
Hi Michelle - To bypass eddy-current correction, you set doeddy = 0 in your config file. See: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula To skip the tensor fit step altogether you use the -notensor option in trac-all. See: http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Processingstepoptions However, this step only takes a couple of minutes, so you don't gain much by skipping it, and instead you might cause trouble for yourself by missing some other files that it generates. The existing options for intra-subejct and inter-subject registration are shown here: http://surfer.nmr.mgh.harvard.edu/fswiki/trac-all#Processingsteps These are the only options currently available. To use another template, we'd have to morph the tracts and anatomical segmentations from the 33 subjects that are included in our atlas to the space of this new template. We'd also have to modify TRACULA to be able to use the morph files that the new registration method generates. Importantly, this may not be worth the trouble. Improving the inter-subject registration by using a different template would not affect TRACULA as much as it would affect a voxel-based method. That's because TRACULA does not use information from the atlas on the exact spatial coordinates of the tract in the template space. It uses information only on what anatomical segmentation labels (cortical + subcortical) the tract goes throuh or next to, at each point along its trajectory. So we're not just morphing tract labels from an atlas onto an individual. Because of how TRACULA works, only a rough alignment to the atlas is sufficient, and improving the registration method doesn't have as big of an impact as you might expect (I've tried). Hope this helps, a.y On Tue, 31 Mar 2015, Michelle T Kassel wrote: Hello, I am interested in using TRACULA for my data, but I have a few questions about modifying the dmrirc configuration file. I have already conducted eddycorrect, bet, and dtifit in FSL, registration of T1 and dti using ANTs, and I have also registered individual subject data to a template created in our lab (rather than MNI_T1_1mm_brain.nii.gz). We tried FSL flirt alignment initially, and it did not work well for our data, thus we used a different program that yielded better alignment for our data, and I'd like to be able to input the data files I have already registered (rather than re-registering them through fsl flirt). Additionally, as I already have the dtifit output, as well as the registration steps complete, I want to ensure that I am specifying the correct parameters in the dmrirc configuration file before running TRACULA on the data. I have set the dtroot, subjlist, dcmroot, dcmlist, bvecfile, and bvalfile to the appropriate locations for our data. I have set doeddy = 0, and was wondering what further specifications I need to provide in the dmrirc configuration file to use my already processed (dtifit) and registered data in the TRACULA steps. I greatly appreciate any assistance with the dmrirc setup. Thank you, Michelle ___ 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-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)
Hi zeke Do you know if version that support non Haswell cpu will be available? Knut Jørgen On 05/22/2015 06:06 PM, Z K wrote: That particular developmental build is compiled with optimization flags for machines containing Intels new Haswell processor and wont run on platforms without it. Although that build is available via our dev download page, it remains an unsupported build that exists primarily for internal experimental purposes only. -Zeke On 05/22/2015 11:49 AM, Knut J Bjuland wrote: Hi I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I start mri_convert on ubuntu 14.04.4 I get this results. knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME= /usr/local/freesurfer60 knutjb@dmed4960:/usr/local/freesurfer60$ source /usr/local/freesurfer60/SetUpFreeSurfer.sh freesurfer-Linux-centos7_x86_64-dev-20150521 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer60 FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/knutjb/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 knutjb@dmed4960:/usr/local/freesurfer60$ mri_con mri_concatmri_concatenate_lta mri_convert_crash mri_concatenate_gcam mri_convert mri_convert_mdh knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert --help Illegal instruction (core dumped) knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert -h Illegal instruction (core dumped) knutjb@dmed4960:/usr/local/freesurfer60$ and in GDB Starting program: /usr/local/freesurfer60/bin/mri_convert [Thread debugging using libthread_db enabled] Using host libthread_db library /lib/x86_64-linux-gnu/libthread_db.so.1. Program received signal SIGILL, Illegal instruction. 0x006be48f in make_cmd_version_string (argc=argc@entry=1, argv=argv@entry=0x7fffdd98, id_string=id_string@entry=0xc6de08 $Id: mri_convert.c,v 1.221 2015/04/16 18:56:00 greve Exp $, version_string=version_string@entry=0xc6cd66 $Name: $, return_string=return_string@entry=0x7fffb0e0 (\rW\366\377\177) at version.c:215 215version.c: No such file or directory. Knut Jørgen Bjuland ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] freesurfer-Linux-centos7_x86_64-dev-20150521 on ubuntu 14.04 crash with Illegal instruction (core dumped)
Were still in discussions about that. If the centos7 build (non-Haswell) does not provide any significant reliability or performance advantages than the centos6 build than we may just continue with the centos6 build. -Zeke On 05/22/2015 02:54 PM, Knut J Bjuland wrote: Hi zeke Do you know if version that support non Haswell cpu will be available? Knut Jørgen On 05/22/2015 06:06 PM, Z K wrote: That particular developmental build is compiled with optimization flags for machines containing Intels new Haswell processor and wont run on platforms without it. Although that build is available via our dev download page, it remains an unsupported build that exists primarily for internal experimental purposes only. -Zeke On 05/22/2015 11:49 AM, Knut J Bjuland wrote: Hi I have tired the freesurfer-Linux-centos7_x86_64-dev-20150521. When I start mri_convert on ubuntu 14.04.4 I get this results. knutjb@dmed4960:/usr/local/freesurfer60$ export FREESURFER_HOME= /usr/local/freesurfer60 knutjb@dmed4960:/usr/local/freesurfer60$ source /usr/local/freesurfer60/SetUpFreeSurfer.sh freesurfer-Linux-centos7_x86_64-dev-20150521 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer60 FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/knutjb/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/share/fsl/5.0 knutjb@dmed4960:/usr/local/freesurfer60$ mri_con mri_concatmri_concatenate_lta mri_convert_crash mri_concatenate_gcam mri_convert mri_convert_mdh knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert --help Illegal instruction (core dumped) knutjb@dmed4960:/usr/local/freesurfer60$ mri_convert -h Illegal instruction (core dumped) knutjb@dmed4960:/usr/local/freesurfer60$ and in GDB Starting program: /usr/local/freesurfer60/bin/mri_convert [Thread debugging using libthread_db enabled] Using host libthread_db library /lib/x86_64-linux-gnu/libthread_db.so.1. Program received signal SIGILL, Illegal instruction. 0x006be48f in make_cmd_version_string (argc=argc@entry=1, argv=argv@entry=0x7fffdd98, id_string=id_string@entry=0xc6de08 $Id: mri_convert.c,v 1.221 2015/04/16 18:56:00 greve Exp $, version_string=version_string@entry=0xc6cd66 $Name: $, return_string=return_string@entry=0x7fffb0e0 (\rW\366\377\177) at version.c:215 215version.c: No such file or directory. Knut Jørgen Bjuland ___ 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] frontal lobe problem on reconstruction
what is a .cshr? do i just type the long command at the command line? sorry if this is a dumb question From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu] Sent: Monday, May 18, 2015 4:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] frontal lobe problem on reconstruction Mia, Hi, what sort of error? I looked at the image in freeview, and it looks like the patient is missing their left frontal lobe. The surfaces look ok in that region given that. btw, to make viewing in freeview easy, add this to your .cshrc, all one line: alias fv freeview -v mri/T1.mgz mri/brainmask.mgz mri/aseg.mgz:colormap=lut -f surf/lh.pial:edgecolor=red surf/rh.pial:edgecolor=red surf/lh.white:edgecolor=blue surf/rh.white:edgecolor=blue then, to use: cd BW30_PreOp_MRI fv it will bring-up the major volumes and surfaces. N. On Mon, 2015-05-18 at 20:02 +, Borzello, Mia wrote: Hi Freesurfers, I ran recon-all and didn't initially get an error. I am not plotting the surface in matlab and am getting an error but am not sure why. Any help would be great! Thanks! 1) BW30 2) recon-all -autorecon1 -autorecon2 -autorecon3 -subjectBW30_SurferOutput -i /autofs/space/huygens_001/users/mia/subjects/BW30_PreOp_MRI/1.3.12.2.1107.5.2.32.35311.2015032512254299614890687.0.0.0/1.3.12.2.1107.5.2.32.35311.2015032512330819010190759.dcm ___ 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: distance between tract sections in pathstats.byvoxel.txt
Hi Celine - In an individual pathstats.byvoxel.txt file, the (x,y,z) coordinates are given for every point along the tract, so you can calculate the distance between consecutive points. If you use trac-all -stat to put stats together across multiple subjects, then in the *.log files generated for each tract under the stats/ directory, you'll find a line like: INFO: Sampling interval along path is [...] Best, a.y On Fri, 24 Apr 2015, Celine Louapre wrote: Hi Anastasia and Tracula experts I did analyses with Tracula using the very nice feature that allows to perform the statistics along the tracts. I reported the result as function of location along the tracts expressed as voxel index, meaning that the first section was voxel index 1, the 2nd tract section was voxel index 2 etc along the entire path. However, I just got a reviewer comment asking for the actual distance between each voxel index. I guess this depends on the voxel size, but maybe also on the curvature of the tract? Is there a simple way to have the average distance between 2 sections along one tract? Thank you Celine ___ 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 reinit
Hi Lars - A path with fewer control points will generally be smoother. So if the tract is pretty much a straight line, you might get a noisier result if you increase the number of control points. But if the tract is more convoluted than a straight line, then you need more control points to define it accurately. So it's hard to predict the result of increasing the control points in general, it depends on the specific case. BTW, if you change the number of control points, you don't need to use the reinit variable - that's only for rerunning with the same control points as before. Best, a.y On Tue, 12 May 2015, Lars M. Rimol wrote: Hi, The various tracts have different default numbers of control points, with a higher number for more curved paths. In a previous mail Dr. Yendiki recommended changing the number of control points if several attempts rerunning reinit don't produce a satisfactory result. Is it always better to have a larger number of control points, except for the increase (I assume) in processing time? Or will a larger number produce a worse result for less curved tracts? yours, Lars M. Rimol, PhD Norwegian University of Science and Technology (NTNU) 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_SNR
There's no perfect way to estimate SNR unfortunately. For example, using
the background outside the brain would mean that you'd be using locations
outside the head coil, and the noise there is not going to be
representative of the noise inside the head coil.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasi,
Thank you very much for your support.
Actually I did. I checked trac-all.log and I found the following command line:
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}'
dwi_snr.txt
Here is the reason for my question:
I know that the SNR can be calculated by the ratio of ( the mean intensity in a
WM area like the corpus callosum (for example) and the standard deviation (or
the mean) for a region in the background outside the brain that does not
contain any artefacts. Then we can add some kind of correction factors to
account for the fact that the noise distribution is not Gaussian
(http://www.ncbi.nlm.nih.gov/pubmed/17622966)
What I noticed in Tracula's command line that it calculate the SNR by dividing
the mean and the standard deviation for an area behind the mask.
That's why I am confused.
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Friday, May 22, 2015 11:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
Hi Mohamad - You can search for dwi_snr in the trac-all.log file to see the
command line that produces this file.
a.y
On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
“dwi_snr.txt” is an output of the preprocessing step in TRACULA.
Kindly how TRACULA is calculating the SNR for every direction in DTI data? Is
there any command line that can do it?
Thanks,
Mohamad
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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_SNR
Hi Anastasia,
I am sure that I am missing something.
Kindly, the purpose of my question is to improve my understanding for this
issue.
SNR is a ratio between signal and noise. Tracula's command line is dividing the
mean intensity for an ROI by the standard deviation for the same ROI so why the
output is ratio between signal and noise? I can't find any evaluation for the
noise in this method.
Looking forward to learn from you
Bests,
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Friday, May 22, 2015 1:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
There's no perfect way to estimate SNR unfortunately. For example, using the
background outside the brain would mean that you'd be using locations outside
the head coil, and the noise there is not going to be representative of the
noise inside the head coil.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasi,
Thank you very much for your support.
Actually I did. I checked trac-all.log and I found the following command
line:
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk
'{print $1/$2}' dwi_snr.txt
Here is the reason for my question:
I know that the SNR can be calculated by the ratio of ( the mean
intensity in a WM area like the corpus callosum (for example) and the
standard deviation (or the mean) for a region in the background
outside the brain that does not contain any artefacts. Then we can add
some kind of correction factors to account for the fact that the noise
distribution is not Gaussian
(http://www.ncbi.nlm.nih.gov/pubmed/17622966)
What I noticed in Tracula's command line that it calculate the SNR by
dividing the mean and the standard deviation for an area behind the mask.
That's why I am confused.
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia
Yendiki
Sent: Friday, May 22, 2015 11:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
Hi Mohamad - You can search for dwi_snr in the trac-all.log file to see the
command line that produces this file.
a.y
On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
“dwi_snr.txt” is an output of the preprocessing step in TRACULA.
Kindly how TRACULA is calculating the SNR for every direction in DTI data?
Is there any command line that can do it?
Thanks,
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] TRACULA_SNR
The mean is the signal, the standard deviation is the noise.
http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
I am sure that I am missing something.
Kindly, the purpose of my question is to improve my understanding for this
issue.
SNR is a ratio between signal and noise. Tracula's command line is dividing the
mean intensity for an ROI by the standard deviation for the same ROI so why the
output is ratio between signal and noise? I can't find any evaluation for the
noise in this method.
Looking forward to learn from you
Bests,
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Friday, May 22, 2015 1:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
There's no perfect way to estimate SNR unfortunately. For example, using the
background outside the brain would mean that you'd be using locations outside
the head coil, and the noise there is not going to be representative of the
noise inside the head coil.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasi,
Thank you very much for your support.
Actually I did. I checked trac-all.log and I found the following command line:
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk
'{print $1/$2}' dwi_snr.txt
Here is the reason for my question:
I know that the SNR can be calculated by the ratio of ( the mean
intensity in a WM area like the corpus callosum (for example) and the
standard deviation (or the mean) for a region in the background
outside the brain that does not contain any artefacts. Then we can add
some kind of correction factors to account for the fact that the noise
distribution is not Gaussian
(http://www.ncbi.nlm.nih.gov/pubmed/17622966)
What I noticed in Tracula's command line that it calculate the SNR by dividing
the mean and the standard deviation for an area behind the mask.
That's why I am confused.
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia
Yendiki
Sent: Friday, May 22, 2015 11:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
Hi Mohamad - You can search for dwi_snr in the trac-all.log file to see the
command line that produces this file.
a.y
On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
“dwi_snr.txt” is an output of the preprocessing step in TRACULA.
Kindly how TRACULA is calculating the SNR for every direction in DTI data? Is
there any command line that can do it?
Thanks,
Mohamad
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[Freesurfer] Postdoctoral Research Scholar Position in Neuroimaging and Behavior Genetic
The Department of Psychiatry at the University of California, San Diego is pleased to invite applications for a postdoctoral research scholar position in neuroimaging and behavior genetics under the direction of Drs. William Kremen (Psychiatry) and Anders Dale (Radiology and Neuroscience). The position focuses on training in the application of sophisticated neuroimaging methods (structural MRI, DTI, fMRI, and ASL) and associated studies that will be applied to the NIH/NIA-funded Vietnam Era Twin Study of Aging (VETSA). VETSA is a unique longitudinal study of middle-aged male twins that focuses on understanding cognitive and brain aging. Over 500 twins have undergone neuroimaging and extensive neurocognitive assessment, personality and psychosocial measures, a medical history interview, in-lab physical health measures, and hormonal assays. Genome-wide genotyping of all participants is currently underway. Wave 3 of the project, which was recently funded, will acquire new longitudinal and neuroimaging data. Applications from many disciplines may be considered, and the position is open to qualified international applicants. Requirements for the position are: 1) completion of relevant Ph.D. research activities within the past five years; 2) advanced neuroimaging and programming skills, 3) statistical knowledge, 4) evidence of writing skills, and 5) an interest in imaging genetics research. Experience with multilevel data analysis and/or genetics is desirable. The postdoctoral candidate will be encouraged to develop his or her own research projects that fit within the overall scope of the VETSA project. The position will entail immersion in MR image analysis and opportunities to learn about twin modeling. Experience with FreeSurfer and/or other neuroimaging software, R, and MATLAB is strongly preferred. This advertisement is for a 2-year appointment beginning immediately. Salary will be consistent with the NIH/NRSA levels in accordance with the University of California, San Diego for Postdoctoral trainees. Compensation includes UCSD benefits, including health insurance and vacation time. Review of applications will begin immediately and will continue until the position is filled. As an Equal Opportunity/Affirmative Action Employer, the UCSD Department of Psychiatry seeks to recruit and retain a diverse workforce as a reflection of our strong commitment to the twin goals of achievement of excellence and diversity among its faculty and staff. We are thus interested in candidates who are committed to the highest standards of scholarship and professional activities, and to the development of a climate that supports equality and diversity. To apply, please send a copy of your CV, a brief statement of research interests and goals, and any selected reprints to the email addresses below. Letters of reference will be required before final approval of hiring. Informal inquiries concerning this position are encouraged. Please e-mail Dr. Anders Dale (amd...@ucsd.edu) and Dr. William Kremen (wkre...@ucsd.edu) for more details. ___ 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_SNR
But in our command line
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk '{print
$1/$2}' dwi_snr.txt
the flag -m is the mean intensity and the flag -s is the standard deviation for
the intensity
Here we are using the same mask White-Matter++.flt.nii.gz so the output is
mean intensity for the signal behind this mask and the standard deviation for
the intensity behind this mask.
Why the standard deviation is noise?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Friday, May 22, 2015 3:15 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
The mean is the signal, the standard deviation is the noise.
http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
I am sure that I am missing something.
Kindly, the purpose of my question is to improve my understanding for this
issue.
SNR is a ratio between signal and noise. Tracula's command line is dividing
the mean intensity for an ROI by the standard deviation for the same ROI so
why the output is ratio between signal and noise? I can't find any evaluation
for the noise in this method.
Looking forward to learn from you
Bests,
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia
Yendiki
Sent: Friday, May 22, 2015 1:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
There's no perfect way to estimate SNR unfortunately. For example, using the
background outside the brain would mean that you'd be using locations outside
the head coil, and the noise there is not going to be representative of the
noise inside the head coil.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasi,
Thank you very much for your support.
Actually I did. I checked trac-all.log and I found the following command
line:
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk
'{print $1/$2}' dwi_snr.txt
Here is the reason for my question:
I know that the SNR can be calculated by the ratio of ( the mean
intensity in a WM area like the corpus callosum (for example) and the
standard deviation (or the mean) for a region in the background
outside the brain that does not contain any artefacts. Then we can
add some kind of correction factors to account for the fact that the
noise distribution is not Gaussian
(http://www.ncbi.nlm.nih.gov/pubmed/17622966)
What I noticed in Tracula's command line that it calculate the SNR by
dividing the mean and the standard deviation for an area behind the mask.
That's why I am confused.
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
Anastasia Yendiki
Sent: Friday, May 22, 2015 11:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
Hi Mohamad - You can search for dwi_snr in the trac-all.log file to see
the command line that produces this file.
a.y
On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
“dwi_snr.txt” is an output of the preprocessing step in TRACULA.
Kindly how TRACULA is calculating the SNR for every direction in DTI data?
Is there any command line that can do it?
Thanks,
Mohamad
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
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Re: [Freesurfer] TRACULA_SNR
Standard deviation is the variation around the mean. The more the noise,
the more the variation.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
But in our command line
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}'
dwi_snr.txt
the flag -m is the mean intensity and the flag -s is the standard deviation for
the intensity
Here we are using the same mask White-Matter++.flt.nii.gz so the output is
mean intensity for the signal behind this mask and the standard deviation for the
intensity behind this mask.
Why the standard deviation is noise?
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki
Sent: Friday, May 22, 2015 3:15 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
The mean is the signal, the standard deviation is the noise.
http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
I am sure that I am missing something.
Kindly, the purpose of my question is to improve my understanding for this
issue.
SNR is a ratio between signal and noise. Tracula's command line is dividing the
mean intensity for an ROI by the standard deviation for the same ROI so why the
output is ratio between signal and noise? I can't find any evaluation for the
noise in this method.
Looking forward to learn from you
Bests,
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia
Yendiki
Sent: Friday, May 22, 2015 1:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
There's no perfect way to estimate SNR unfortunately. For example, using the
background outside the brain would mean that you'd be using locations outside
the head coil, and the noise there is not going to be representative of the
noise inside the head coil.
On Fri, 22 May 2015, Alshikho, Mohamad J. wrote:
Hi Anastasi,
Thank you very much for your support.
Actually I did. I checked trac-all.log and I found the following command line:
fslstats -t dwi.nii.gz -k White-Matter++.flt.nii.gz -m -s | awk
'{print $1/$2}' dwi_snr.txt
Here is the reason for my question:
I know that the SNR can be calculated by the ratio of ( the mean
intensity in a WM area like the corpus callosum (for example) and the
standard deviation (or the mean) for a region in the background
outside the brain that does not contain any artefacts. Then we can
add some kind of correction factors to account for the fact that the
noise distribution is not Gaussian
(http://www.ncbi.nlm.nih.gov/pubmed/17622966)
What I noticed in Tracula's command line that it calculate the SNR by dividing
the mean and the standard deviation for an area behind the mask.
That's why I am confused.
Mohamad
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of
Anastasia Yendiki
Sent: Friday, May 22, 2015 11:43 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA_SNR
Hi Mohamad - You can search for dwi_snr in the trac-all.log file to see the
command line that produces this file.
a.y
On Mon, 30 Mar 2015, Alshikho, Mohamad J. wrote:
Hi Anastasia,
“dwi_snr.txt” is an output of the preprocessing step in TRACULA.
Kindly how TRACULA is calculating the SNR for every direction in DTI data? Is
there any command line that can do it?
Thanks,
Mohamad
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Tracula data and ICV
Hi Alan - If you were analyzing a volume (or area or length) measure, it'd make sense to include something like ICV. If you're analyzing an anisotropy or diffusivity measure, you wouldn't expect those to be affected my how big the head is. Best, a.y On Sat, 25 Apr 2015, Alan Francis wrote: Dear Anastasia: Hope all is well. I have done tracula analysis on 75 brains (HARDI) and I am statistically analyzing the data. Do I need to use ICV as a covariate in my statistical model? thank you, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| Alan N. Francis PhD NIDA T32 Fellow in Drug Abuse Brain Imaging Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu afran...@mclean.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 prep help
Hi Efrat - I'm guessing that you specified in your config file that you want to perform B0 field inhomogeneity correction (set dob0 = 1) but perhaps did not specify the B0 field map magnitude files correctly (set b0mlist = ...) I'm guessing this because of this line in your log: mri_convert / /mnt/hgfs/linux_share/subjects/TB_400/dmri/b0mag.nii.gz It thinks the field map file is called / and it fails to convert it. If you didn't really want to use field maps, you can remove that from your config file. Best, a.y On Wed, 13 May 2015, Efrat Kliper wrote: Dear Freesurfer experts, I have encountered the following error while running the tracula pre-processing command and was hoping you could help me understand how to correct this. from the log file INFO: input image orientation is LPS INFO: input image determinant is 3.51562 fslswapdim /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig.nii.gz x -y z /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_or ig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig_flip.nii.gz INFO: found /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig_flip.mghdti.bvecs /mnt/hgfs/linux_share/subjects/TB_400/dmri/bvecs mv -f /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig_flip.mghdti.bvals /mnt/hgfs/linux_share/subjects/TB_400/dmri/bvals mri_convert / /mnt/hgfs/linux_share/subjects/TB_400/dmri/b0mag.nii.gz mri_convert / /mnt/hgfs/linux_share/subjects/TB_400/dmri/b0mag.nii.gz corRead(): can't open file /COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /... Thanks Efrat ___ 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 about error message when run 'Tracula'
Hi Xiaofu - The bedpostx program is not configured to run on any type of cluster with any type of queueing software. It was originally written to be run on an SGE cluster with specific queue names. The bedpostx_mgh is a modified version that also works on our PBS cluster. Making it work on additional clusters would require additional tweaks, and it's impossible for us to make it work on everyone's cluster. In a future version, I'd like to give the option to simply print out all the necessary commands, and then it would be up to the user to figure out how to submit them as jobs on their own cluster. This is not implemented yet. a.y On Tue, 19 May 2015, Xiaofu wrote: Dear Sir/Madam, I tried to run Tracula in the C2B2 server at Columbia University. However, I got the following error message after submitted my job using qsub to the sever. I'd greatly appreciate it if you could help me resolve this problem. WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /DTIdata/Tracula/3789/dmri subjectdir is /DTIdata/Tracula/3789/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. 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.
