Freesurfer July 2014

freesurfer@nmr.mgh.harvard.edu

163 participants
257 discussions

Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 20 Dec '17

20 Dec '17

Hi Anastasia, Yes, i am running this on ubuntu 12.04. Sincerely, Florian >>> Anastasia Yendiki 20.08.13 17.38 Uhr >>> Hi Florian - Are you running this on an ubuntu system by any chance? a.y On Tue, 20 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Thank you for your help. > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command "xfmrot" changed the dots back to > commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the > system language everything was genereted correctly and trac-all -prep ran without any errors. > I'm so glad. > > Then, I started the next step "trac-all -bedp" and got a syntax error "/usr/local/freesurfer/bin/bedpostx_mgh: 131: > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I also attached the the logfile. I was reading > about this error in the mail archive. Would I have to run "bedpostx" outside of tracula ? > > Sincerely, > Florian > > >>> Anastasia Yendiki 19.08.13 17.54 Uhr >>> > > Hi Florian - Can you please change the decimal commas to points and try > again? > > a.y > > On Mon, 19 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia, > > > > Here are the bvec and bval files you asked me about. > > > > Sincerely, > > Florian > > > > >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> > > > > Hi Florian - Can you please also attach the bvecs/bvals files from the > > dmri directory? > > > > Thanks, > > a.y > > > > On Sun, 18 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia, > > > > > > Thanks for your help. I renamed the directories and reran trac-all. It > > > worked for the moment. > > > However, then I got another error: "bvecs and bvals don't have the same > > > number of entries." > > > I don't know why, because they actually have the same number of entries. > > > > > > I attached the logfile so that you may see what is going on. The error > > > occours at line 1463. > > > > > > Thank you in advance for your help. > > > > > > Sincerely, > > > Florian > > > > > > > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > > > > > Hi Florian - I see what's going on. Can you please rename the directory > > > /data/physics/florian/nii into something that doesn't include "nii", and > > > rerun? Because "nii" is a file extension, this confuses some of the > > > scripts. > > > > > > Thanks, > > > a.y > > > > > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > > > > > Hi Anastasia > > > > > > > > I ran the command you sent me and it runs without any errors. > > > > I also attached the command line for you. > > > > > > > > Furthermore i ran data with 12 diffusion directions and i keep getting the > > > > same kind of problems. > > > > > > > > sincerely > > > > Florian > > > > > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr > > > >>> > > > > > > > > Hi Florian - Can you please run this command directly on the command line > > > > and see if there are any errors? > > > > > > > > flip4fsl > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > > > > > > > Thanks, > > > > a.y > > > > > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > > > > > > > Hi Anastasia > > > > > > > > > > Thank you for your answer. > > > > > > > > > > Yes, those files exist. > > > > > I also extracted the bvec an bval files with anotther software then > > > > dcm2nii > > > > > and i keep getting the same kind of error. > > > > > Also, about the 6 diffusion direction, those data i sent you, are just > > > > > testdata for running tracula. > > > > > > > > > > sincerely > > > > > Florian > > > > > > > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr > > > >>> > > > > > > > > > > Hi Florian - Do these files exist? > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec > > > s > > > > > > > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > > > s > > > > > > > > > > > > > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and > > > this > > > > > has nothing to do with the error you're getting) I have to warn you that > > > > > you may not be able to get good results running probabilistic > > > tractography > > > > > on this data. It looks like you're acquiring the same 6 diffusion > > > > > directions, repeated 8 times. Six directions is the absolute minimum for > > > > > reconstructing the tensor model, but will probably not be sufficient for > > > > > the crossing fiber model that bedpostx reconstructs (and is used by > > > > > tracula). Your scan time is better spent acquiring 48 different > > > > > directions, rather than the same 6 directions 8 times. > > > > > > > > > > a.y > > > > > > > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > > > > > > > Hello, > > > > > > > > > > > > I have been trying to run tracula on my data and i keep getting the > > > same > > > > > > kind of error repeatedly. > > > > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > > > > diffusion protocol. However, tracula cannot read the bvec and bval > > > data > > > > > out > > > > > > of the dicom header. Therefore, I implemented bvec and bval files into > > > > the > > > > > > config file. > > > > > > After doing so, I got the error which says that tracula cannot find > > > the > > > > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > > > > I have tried many options, but still cannot find a solution. > > > > > > I am hoping to get some troubleshooting help. > > > > > > > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > > > > files. > > > > > > To uphold patient confidentiality, I have encode the name patient's > > > data > > > > > as > > > > > > "AAAAAA". > > > > > > > > > > > > I believe the problems are the bvec and bval files or their > > > structures. > > > > > The > > > > > > log-file lete me assume this, especially the lines 202 - 205, 264 - > > > 268 > > > > > and > > > > > > 1480 - 1484. > > > > > > > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > > > > > > > With kind regards, > > > > > > > > > > > > Florian Borsodi > > > > > > Department of Neurology > > > > > > Medical University of Graz > > > > > > > > > > > > > > > > > > > > > > > > > > > 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(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Raw Cortical thickness values
by Muhammad Naveed Iqbal Qureshi 06 Jul '17

06 Jul '17

Dear Community, I need to know how can I read the numeric cortical thickness values from freesurfer processed files. (as there are too many in the surf folder) Thank you. Best Regards Naveed

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mri_cvs_register failure from missing shared lib
by Michael Waskom 25 Apr '17

25 Apr '17

Hi, I had mri_cvs_register die on me when it couldn't find a shared library. Relevant bit is (full log is attached): mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory Freesurfer bugr info: -------------------- FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64 ---------------------- Any thoughts on how to proceed? Thanks! Michael

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FSFAST mkcontrast-sess with spmhrf 2 question
by Joseph Dien 25 Mar '16

25 Mar '16

Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com//

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some questions about optseq
by charujing123 15 Jan '16

15 Jan '16

Hi FS experts, I try to design the schedule by optseq2. However it is beyond my ability as our experiment has a little complicated. Here is our goal: two successive trials decide condition. For example, this is our sequence:2 2 1 1 2 2 2 1 1 2 2 1 2 1 1 2 1 2 2 1 1 1 1 2 2 2 2 1 1 1 2 1 2 1 1 1 1 1 1 2 1 2 1 2 1 2 1 2 2 1 1 2 2 2 2 2 2 1 1 1 2 2 2 1 2 2 2 2 1 2 2 1 1 2 1 1 2 1 1 1 2 .22 and 11 is the same condition(this condition has 40 repeats); 12 and 21 is the same condition(this condition also has 40 repeats). That is to say, there are two conditons in this run. 81 trials in this run, and each trial has 1.5s intervels. And mean intertrial intervals is 3.5s. Our TR is 2s. According the efficiency about these two conditions, how could I design the intertrial intervals to get a appropriate sequence? I tried this: optseq2 --ntp 203 --tr 2 --psdwin 0 20 --ev ev1 2 40 --ev ev2 2 40 --nkeep 2 --o ex2 --nsearch 1000 Although it echo a result, I know, it is not what I need, because of every condition having two trials. So how I complete that? Thanks. All the best. Rujing Zha 2014-06-20 charujing123

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DEPRECATED warning in Freesurfers
by Peter Wendorff 13 Oct '15

13 Oct '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I'm working with freesurfer as a software developer in a cloud project. My task is to enable control of freesurfer via network (e.g. REST interfaces). That works fine so far, but I stumbled over the following pearl deprecated warning: "Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer//mni/bin/sharpen_volume line 153." Which has been printed to the log files repeatingly. I'm not a pearl expert, but I think, it's due to a more up to date pearl version used here, that deprecated the usage of ? delimiters for patterns without explicit operator. Using / as a delimiter works fine. I changed that locally to (new line 153): ($output_volume =~ /^([\S]+).mnc/) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; (the original code here was): ($output_volume =~ ?^([\S]+).mnc?) && ($base_name = $1) || die "sharpen_volume failed: output volume does not appear to be" ." a minc volume.\n"; I'm not sure this is the best solution. It's even not strictly necessary to change this - it's only a warning that's thrown; but I think, it's useful. How can I submit this as a patch? Is it enough to report here? What to do? regards Peter Wendorff P.S.: For referene the header parameters of my sharpen_volume for revision comparison: #---------------------------------------------------------------------------- #$RCSfile: sharpen_volume.in,v $ #$Revision: 1.1 $ #$Author: bert $ #$Date: 2003/04/16 14:29:34 $ #$State: Exp $ #--------------------------------------------------------------------------- # ------------------------------ MNI Header - ---------------------------------- #@NAME : sharpen_volume #@INPUT : #@OUTPUT : #@RETURNS : #@DESCRIPTION: modifies intensities so as to produce a sharper histogram #@METHOD : #@GLOBALS : #@CALLS : #@CREATED : February 28, 1996 #@MODIFIED : #----------------------------------------------------------------------------- -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlGTa5kACgkQi8ffXNvWmYSCUQCghMg1EffqfeJK4PSfo20uF8/J H0MAnjJc0WbHPf5gLDUw70K8fnQPjS+L =g+6e -----END PGP SIGNATURE-----

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PhD position in tractography validation, Inserm U930 "Brain and imaging" lab, University François-Rabelais of Tours
by Frédéric Andersson 06 Oct '14

06 Oct '14

"A funded PhD Student position will be available in the “Brain and Imaging” Inserm unit (national institute for health) settled in Tours, France, from October 1st, 2014 to September 30th, 2017. During this time period, the candidate will have: (1) to develop tools and pertinent criteria for comparison of MR-based tractography results to data obtained from dissection; (2) to compare different algorithms used for MR-based tractography; (3) to develop a tool aiming to help decision making for the choice of optimal algorithms and parameters used for tractography. This work will be co-directed by Pr C Destrieux (Anatomist) and Pr G Venturini (Computer Science) in the university of Tours. It will be funded for the whole time period by a grant we obtained from the Ministry of Research (about 1400 € per month). Potential candidates have to send a letter and a CV to christophe.destrieux(a)univ-tours.fr and gilles.venturini(a)univ-tours.fr before the 15th of April. After an internal selection of the applications, they will have to defend their candidateship during an interview organized by the Doctoral School of the university at the end of May 2014."

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Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
by Douglas Greve 25 Sep '14

25 Sep '14

Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: > Dear Dr. Greve, > > Is it possible to register a nonstructural MR sequences (e.g. an ADC > map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, > using the segmentation from the aseg (or aparc+aseg) file to output a > mean ADC value for each anatomic area segmented? > > Thank you for your time and consideration. > > Best wishes, > > Sal > > Salil Soman, MD, MS

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FLAIR Registration Problems
by Zamroziewicz, Marta Karolina 21 Aug '14

21 Aug '14

Hello, This email is related to the archived “bbregister and FLAIR” email chain posted by Kayle Sawyer on 5/23/2014 (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg36117.html) We have also been registering with FLAIR scans, and have run into a problem with approximately half of our subjects. Recon-all completes successfully but a bad registration step leaves our MPRAGE and FLAIR scans misaligned. I’ve attached two screenshots, the first of which shows a bad registration and the second of which shows a good registration. Per your previous suggestion, we ran bbregister using the following flag: bbregister --s SLOTS007 --mov flair.mgz --init-header --reg reg.test.dat --t2 --lta reg.test.lta This did result in a good registration, and we are hoping to incorporate this into our processing pipeline to ensure that we can use the FLAIR for refining the pill surface. The problem that we’ve run into is that we aren’t sure at which point this bbregister step occurs within the recon-all process flow. We were thinking there are a couple of possibilities: 1. manually create the transformation matrix for the FLAIR using the command mentioned above, and then re-run whichever steps necessary in recon-all to include this manually created xform; 2. apply the manually created xform to the mri/orig/FLAIRraw.mgz image to create a new, properly aligned mri/FLAIR.mgz, and then re-run recon-all with whatever steps/flags we need to include this FLAIR image to refine the pial surface. Unfortunately we're not exactly sure which flags to include in recon-all in order to most efficiently re-process our data with the manually created FLAIR transformation, and we were hoping you might offer some advice on this point. Please let me know if I can provide any additional information. Thanks for your time and assistance! [cid:D837E275-197C-46BB-A1D4-B7559DF58D48@beckman.uiuc.edu][cid:D62F65DB-AF9A-4ADC-A596-79E0821DE24D@beckman.uiuc.edu] Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzamro2(a)illinois.edu<mailto:mzamro2@illinois.edu> 815-980-3882

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Diffusion analysis qs
by Rotem Saar 18 Aug '14

18 Aug '14

Dear Anastasia, I followed your suggestion: I calculated the FA maps in freesurfer using the script below (see last message): I did it with both the rotated and the not rotated gradient table. The FA maps were identical as u said. BUT ! - when I used the rotated gradient table in FSL and tried to create the FA & MD maps (as in the first step of tracula), I got the attached results: http://tinypic.com/r/skzwqa/8 Does this map seems ok to u ? I think that something is wrong but can't specify what. I will appreciate your help here again:) ____________________________________________________________________ Hi Rotem - The FA values are actually invariant to a rotation of the gradient vectors. You can test that yourself. If, however, you get different FA maps with the different gradient tables, then something else is going on and not a simple rotation. a.y On Wed, 23 Jul 2014, Rotem Saar wrote: > Dear Anastasia & Michael, > > Thank u for your answers (I attached my last email and your answers at the > end of this email. > > I still want to specify my question. If I only want to extract FA values > using the following script (see script below), and I know that an angle was > applied during the dMRI scans, should I use the rotated gradient matrix ? > > When I first analyzed 20 subjects with the gradient matrix that is published > for a T3 Philips magnet (I also read the gradients from the dicom header - > they were the same) I got reasonable results - but now I don't know what to > think of them... > > source ~/Desktop/fs_script > > dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s > Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval > /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec > > To check results, run: > > tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii > --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii > > tkregister2 --s fsaverage --surf white --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii > /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/mri/ brain.mgz/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii:reg= register.dat:colo > rmap=heat:heatscale=.2,.2,1 > > tkmedit Anatomy0207?orig.mgz -aux brain.mgz -seg wmparc.mgz -reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??????????? --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/ wmparc.mgz > \ > ??????????? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > ??????????? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ > ??????????? --targ > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ > ??????????? --inv --interp nearest --o > /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ > ??????????? --reg > /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ > ???????????/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+ aseg2diff.mgz:colormap > =lut > > > mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ > ???????? /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ > ???????? /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz > > > freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa- masked.mgz/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+ aseg2diff.mgz:colormap > =lut > > mri_segstats --seg > /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i > /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum > /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked > > It'd be nice if things were that simple, but! > > Although the pre-processing is done with FSL tools, tractography is done > with locally written code. Some gradient sets may appear to work with FSL, > but they won't work for us. For example, some dicom converters may perform > a L-R flip as preparation for feeding the gradient vectors into FSL. We > need the unflipped vectors because, instead of flipping vectors, we > convert both vectors and images to LAS orientation. This ensures that they > work both for FSL and for us, and that you can view things correctly in > both freeview and fslview, without the subject looking like it's hanging > upside down from its bat cave or some such awkward arrangement. > > In the end, the best way of knowing that the gradient table is correct is > to run one example subject through and view the eigenvectors of the > tensors as lines to see if they're pointing in the right direction. (Even > though the tensors themselves aren't used for tractography, they're good > for troubleshooting.) > > On Mon, 21 Jul 2014, Harms, Michael wrote: > > > > > FS uses FSL tools under the hood, so you want to use the bvecs that are > > rotated into the axes of the scan. > > > > cheers, > > -MH > > > > --? > > Michael Harms, Ph.D. > > ----------------------------------------------------------- > > Conte Center for the Neuroscience of Mental Disorders > > Washington University School of Medicine > > Department of Psychiatry, Box 8134 > > 660 South Euclid Ave. Tel: 314-747-6173 > > St. Louis, MO ?63110 Email:?mharms@wustl.edu > > > > From: Rotem Saar <saar.rotem(a)gmail.com> > > Reply-To:?Freesurfer?support list <freesurfer(a)nmr.mgh.harvard.edu> > > Date: Monday, July 21, 2014 1:54 PM > > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > > Subject: [Freesurfer] Diffusion analysis qs - gradient matrix > > > > Dear?freesurfer?experts, > > > > For diffusion analysis in?freesurfer?- I want to know which gradient > matrix > >?freesurfer?expects. > > > > The thing is - when I look at the gradient matrix created using a MATLAB > > script that reads the directions from the dicom header - I get one table, > > but the bvecs file created in MRIconvert (for converting dicoms to nifti) > > looks different. > > > > This is the situation when an angle is applied during the acquisition of > the > > dMRI scans, which means that each subject has its own gradient matrix. > > > > So my question is which table should I use for diffusion analysis in > >?freesurfer? The one that was created from the dicom header or the one > > created for NIFTI format using MRIconvert ?? Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel

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Freesurfer July 2014