Freesurfer

freesurfer@nmr.mgh.harvard.edu

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 12 Aug '13

12 Aug '13

When you apply a rotation to the DWIs (as eddy_correct does), you need to apply the same rotation to the corresponding gradient vectors. See for example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated when correcting for subject motion in DTI data. Magn Reson Med 61 (6), 1336–49. If you don't want to pass the dicoms to trac-all directly, you can use mri_convert to convert from dicom to nifti. On Fri, 9 Aug 2013, Soto, David wrote: > hi - am afraid not because I am feeding to trac-all > already eddycorrected images then in the config file > I have > > # Perform registration-based eddy-current compensation? > # Default: 1 (yes) > set doeddy = 0 > # Rotate diffusion gradient vectors to match eddy-current compensation? > # Only used if doeddy = 1 > # Default: 1 (yes) > > is this critical?? > > unfortunately, this is the only way I manage to get it to work > as said my diffusion outputs from mriconverter > are not read by FS, only through mediation > of some FSL operation on the files, then FS > likes those. > > I could start from scratch using dicoms but would prefer > not to as the data is already well organised > > cheers > ds > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: 09 August 2013 22:44 > To: Soto, David > Subject: Re: [Freesurfer] trac-all inquiry > > Are you rotating the gradient vectors accordingly? This is done in > trac-all after running eddy_correct. > > On Fri, 9 Aug 2013, Soto, David wrote: > >> Hi Anastasia, stuff is running smoothly at last one quick question, is there >> any 'disadvantage' in >> using FSL to do the eddy correct and then feed >> those images to trace-all ? >> cheers >> ds >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> >> On 9 Aug 2013, at 15:33, David Soto <dsoto(a)imperial.ac.uk> >> wrote: >> >> hi, for some reason FS does not like the >> nii file from Mriconverter, ( I saw >> a post about this >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html >> ) but does like >> the nii.gz outputs from FSL... >> >> I'll try to debug the bepostx error >> >> thanks! >> >> ds >> >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> On 09/08/13 14:26, Anastasia Yendiki wrote: >> >> There is no reason to conevrt to .mnc. You should use your >> original .nii, if that shows up correctly in freeview. >> >> As for the bedpostx error, this is an Ubuntu issue that >> has come to my attention very recently. In Ubuntu /bin/sh >> is not a bash shell any more. To get around this, you'll >> have to edit the first line of the scripts >> $FREESURFER_HOME/bin/bedpostx_mgh and >> $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace >> "/bin/sh" with "/bin/bash" on the first line of those two >> scripts. >> >> On Fri, 9 Aug 2013, David Soto wrote: >> >> hi- I tried to convert from nii to mnc becos >> that is what i did when >> I did recon-all >> >> but I also tried with nii at the beggining and >> got the same issues. >> In fact in my last post (pasted below >> again)the input was a nii file >> could you please check the stuff below? >> thanks! ds >> >> >> Hi, further to my prior email >> I made some progress. I noted that nii2mnc >> does not seem to work on the diffusion >> output.nii that I got from Mriconverter as the >> output.mnc brain has parts chopped in >> Freeview. >> >> (I think there may be something funny about >> this, as the recon-all does like the T1 output >> form Mriconverter) >> >> HENCE I tried use the output of eddycorrect >> from FSL (which I already run for other thing) >> Then I created a new folder where i placed the >> output of FSL eddycorrect and in the >> configuration file I did >> (i) set dcmlist = >> (fsleddycorrectoutput.nii.gz) >> (ii) turned 'set doeddy = 0' >> >> then run it >> trac-all -c traculatest.txt -prep -log >> trac_from_fsleddy >> >> >> it seemed to complete without errors (log >> attached)n and I checked the preprocessing >> outputs in Freeview (FA, masks and >> aparc+asegs) and all seemed >> fine. >> >> However when I attempt the next stage in >> trac-all >> i.e. trac-all -c traculatest.txt -bedp -log >> trac_from_fsleddy_bedp >> it fails saying the following >> /usr/local/freesurfer/bin/bedpostx_mgh: 131: >> /usr/local/freesurfer/bin/bedpostx_mgh: Syntax >> error: "(" unexpected >> >> >> the log is also attached. >> >> any advise appreciated! >> >> cheers >> ds >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> On 09/08/13 14:02, Anastasia Yendiki wrote: >> >> Why are you converting from .nii >> to .mnc? Why are you not using the >> .nii directly? >> >> On Fri, 9 Aug 2013, David Soto >> wrote: >> >> hi - thanks for the >> feedback >> >> weirdly, the nii2mnc >> transform of the >> diffusion >> data falters, I get a >> part of the brain >> chopped >> have no idea why this >> is the case, as it >> worked fine >> before for the T1 for >> recon-all...I am using >> Ubuntu 12.04 >> >> anyway am trying to >> sort this out now, if >> you have any >> advise that would much >> appreciated!! >> cheers >> ds >> >> >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> On 08/08/13 17:03, >> Anastasia Yendiki >> wrote: >> >> Hi David - >> The fact >> that it's >> taking so >> many tries >> to >> initialize >> the left >> ILF tells >> me that >> something >> has gone >> wrong with >> the data, >> either >> with the >> T1 to DWI >> registration, >> or with >> the mask, >> or >> something >> like that. >> Have you >> looked at >> any of the >> output >> files of >> the >> pre-processing? >> The FA >> map, the >> aparc+aseg, >> etc? >> >> a.y >> >> On Wed, 7 >> Aug 2013, >> Soto, >> David >> wrote: >> >> Hi >> Anastasia, >> I >> checked >> the >> becs >> and >> bvals >> files, >> there >> was >> a >> bug >> in >> the >> transposition >> of >> the >> columns >> into >> 3 >> rows >> in >> the >> bvecs. >> But >> i >> still >> have >> problems.. >> I >> rerun >> trac-all >> -prep >> and >> seemed >> fine >> but >> ended >> with >> a >> Segmentation >> fault >> (core >> dumped) >> which >> however >> is >> not >> present >> in >> the >> last >> line >> of >> the >> trac-all.log >> (Attached). >> Writing >> output >> files >> to/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn >> i_bbr_* >> Writing >> spline >> volume >> to/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mn >> i_bbr_cpts_5.nii.gz >> Segmentation >> fault >> (core >> dumped) >> Just >> in >> case >> I >> tried >> trac-all >> -bedp >> complains >> like >> these >> below, >> any >> advise >> appreciated, >> cheers >> - >> ds >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/tracula02ST.txt >> -bedp >> INFO: >> SUBJECTS_DIR >> is >> /home/dsoto/Documents/fmri/rsdtianawmgui >> INFO: >> Diffusion >> root >> is >> /home/dsoto/Documents/fmri/rsdtianawmgui >> Actual >> FREESURFER_HOME >> /usr/local/freesurfer >> 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 >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri >> /usr/local/freesurfer/bin/bedpostx_mgh: >> 131: >> /usr/local/freesurfer/bin/bedpostx_mgh: >> Syntax >> error: >> "(" >> unexpected >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> >> ________________________________________ >> From: >> Anastasia >> Yendiki >> [ayendiki(a)nmr.mgh.harvard.edu] >> Sent: >> 07 >> August >> 2013 >> 17:22 >> To: >> Soto, >> David >> Cc: >> freesurfer(a)nmr.mgh.harvard.edu >> Subject: >> RE: >> [Freesurfer] >> trac-all >> inquiry >> >> Hi >> David >> - >> Every >> time >> you >> run >> trac-all, >> the >> results >> get >> appended >> to >> this >> file, >> so >> you >> need >> to >> look >> for >> error >> messages >> only >> in >> the >> more >> recent >> invocation >> of >> trac-all. >> The >> first >> error >> there >> seems >> to >> be: >> >> >> Error: >> bvecs >> and >> bvals >> don't >> have >> the >> same >> number >> of >> entries >> >> Do >> you >> have >> the >> same >> number >> of >> b-values >> and >> gradient >> vectors >> and >> volumes >> in >> your >> DWI >> series? >> >> a.y >> >> On >> Tue, >> 6 >> Aug >> 2013, >> Soto, >> David >> wrote: >> >> hi >> >> I >> upgraded >> to >> FS >> 5.3 >> but >> still >> encountering >> issues >> with >> trac-all >> prep. >> >> The >> log >> is >> attached, >> things >> I >> noted >> after >> inspecting >> it >> >> 1) >> INFO: >> FreeSurfer >> build >> stamps >> do >> not >> match >> Subject >> Stamp: >> freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >> Current >> Stamp: >> freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 >> >> 2) >> Error: >> input >> image >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb >> not >> valid >> 3) >> Image >> Exception >> : >> #22 >> :: >> ERROR: >> Could >> not >> open >> image >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain >> 4) >> Image >> Exception >> : >> #22 >> :: >> ERROR: >> Could >> not >> open >> image >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++. >> 5) >> ERROR: >> Could >> not >> read >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz >> but >> despite >> all >> this >> it >> says: >> trac-preproc >> finished >> without >> error >> at >> Tue >> Aug >> 6 >> 21:27:30 >> BST >> 2013 >> >> thanks >> for >> your >> help >> >> cheers >> ds >> >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> >> >> >> >> ________________________________________ >> From: >> Anastasia >> Yendiki >> [ayendiki(a)nmr.mgh.harvard.edu] >> Sent: >> 06 >> August >> 2013 >> 19:30 >> To: >> Soto, >> David >> Cc: >> freesurfer(a)nmr.mgh.harvard.edu >> Subject: >> RE: >> [Freesurfer] >> trac-all >> inquiry >> >> I >> see, >> you're >> using >> the >> old >> version >> of >> tracula >> (from >> freesurfer >> 5.1). >> In >> that >> version, >> you >> had >> to >> define >> the >> number >> of >> low-b >> images >> in >> the >> configuration >> file. >> I >> strongly >> recommend >> updating >> to >> freesurfer >> 5.3. >> A >> lot >> of >> things >> have >> improved >> in >> tracula >> since >> then. >> >> Also, >> in >> the >> future >> please >> attach >> any >> log >> files >> as >> separate >> attachments >> instead >> of >> pasting >> them >> into >> the >> body >> of >> your >> email >> - >> this >> causes >> the >> body >> of >> the >> email >> to >> exceed >> the >> limit >> allowable >> on >> the >> list. >> >> Thanks, >> a.y >> >> >> 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. >> >> >> >> >> >> >> >> >> >> >> >> >> > > >

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Re: [Freesurfer] Setting up enviornment variable permenantly
by Bruce Fischl 11 Aug '13

11 Aug '13

can you cc the list so that others can help? Have you looked for the file: ~/.tchsrc it won't show up in ls unless you specify the -a option (all I think) as the dot files are hidden by default. Bruce On Sun, 11 Aug 2013, Muhammad Naveed Iqbal Qureshi wrote: > Hi, I am using Ubuntu 12.04 and using tcsh computer specs are core i7 3.6ghz with 32 gb ram > > Thank you > > Best Regards, > Muhammad Naveed Iqbal Qureshi > > On 11-Aug-2013, at 10:20 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Naveed >> >> what kind of computer are you using? The .cshrc would be in your home directory. Do you know what shell you are running? >> Bruce >> >> >> On Sun, 11 Aug 2013, Muhammad Naveed Iqbal Qureshi wrote: >> >>> Hello, >>> >>> I am unable to find the .tcshrc files. Where can I find it. >>> >>> I am unable to follow this process as stated on the website. >>> >>> Alternately, the resource file for the shell can be configured to source the >>> file automatically each time the shell is started. In the home directory of >>> the user who will be running FreeSurfer binaries, edit the file .cshrc if >>> C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for >>> Bash, and .profile for sh, to include the previous two lines (which setenv >>> FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script). >>> >>> Best Regards, >>> Naveed >>> >>> >> >> >> 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. > > >

5 6

surface to volume
by Fernando Valle-Inclán 11 Aug '13

11 Aug '13

Hi freesurfers, Is it possible to transform the statistical results of a surface analysis into an anatomical volumen? I've been reading about tkregister2 and mri_surf2vol, but I'm not confident. Any help would be appreciated Fernando Valle-Inclan

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Setting up enviornment variable permenantly
by Muhammad Naveed Iqbal Qureshi 11 Aug '13

11 Aug '13

Hello, I am unable to find the .tcshrc files. Where can I find it. I am unable to follow this process as stated on the website. Alternately, the resource file for the shell can be configured to source the file automatically each time the shell is started. In the home directory of the user who will be running FreeSurfer binaries, edit the file .cshrc if C-shell will be used, the .tcshrc for enhanced C-shell, the .bashrc file for Bash, and .profile for sh, to include the previous two lines (which setenv FREESURFER_HOME, and then source the SetUpFreeSurfer.csh(or sh) script). Best Regards, Naveed

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Re: [Freesurfer] nu.mgz intensity too dark
by Bruce Fischl 09 Aug '13

09 Aug '13

Hi Abid you can run recon-all -make all -s .... and that should do it (since the timestamp on the orig has changed) cheers Bruce On Fri, 9 Aug 2013, Abid Qureshi wrote: > Hi Dr. Fischl, > I've changed the intensity on the orig.mgz files so that there is better > differentiation between white matter and gray matter. Then do I restart > recon-all after a certain step in the process? How does recon-all know to > use the newly modified orig.mgz file. > > Thanks, > Abid > > > On Thu, Aug 8, 2013 at 9:54 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Abid > > --scale specifies a floating point number to multiply each voxel > intensity by, so --scale 0.5 will make every intensity half as > much > > cheers > Bruce > > > On Thu, 8 Aug 2013, aqureshi(a)nmr.mgh.harvard.edu wrote: > > When I looked at orig.mgz it is actually too bright. It's > very hard to > differentiate white and gray matter from how bright the > image is. Maybe > that is the root of the problem. I tried correcting it > with mri_convert > like this: > > cp orig.mgz holder_orig.mgz > mri_convert --scale 3 holder_orig.mgz orig.mgz > > But scale 2-5 all increase the brightness further, which > would probably > worsen the problem. I wasn't able to find how to decrease > brightness (or > increase contrast) in mri_convert --help. How would I > decrease the > brightness? It does not take negative numbers (like -3). > > Thanks, > Abid > > > > ------------------ > > maybe try scaling up the orig.mgz then? I never really > understood why the > nu darkens it sometime. Alternatively you could scale up > the nu, but you > will have already lost dynamic range > > ------------------ > > The 001.mgz actually looks good in this case > (in terms of intensity) so > I'm not sure if it makes sense to scale it up > further. The problem is with > the nu.mgz being too dark. I'll try it out > though if you think it will > also work in this case. > > - Abid > > > --------------- > > you could try using --scale <scale factor> to > scale the intensities of the > 001.mgz up > > --------------- > > Hi Dr. Fischl, > > I had a couple subjects that > failed recon-all. Although the > error log > said > recon-all failed at mri_watershed > it looks like the root problem is > a > couple steps earlier, because the > nu.mgz looks too dark. This was > discussed in a previous thread > from 2008. > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html. > > You wrote, "p.s. are the 001.mgz > and 002.mgz dark? The orig.mgz? > Sometimes > nu_correct can create very dark > images, and there are some > switches you > can loo through to correct them. > Alternatively if it is the > 001.mgz, > mri_convert has a scale option you > can use." > > On my subject 001.mgz looks good > (there was no 002.mgz file). It is > only > nu.mgz that looks too dark. It > looks like the solution you gave > then was > for a problematic 001.mgz file, > but from your response it looks as > if > the > problem was nu.mgz the solution > would be different. What are the > switches > you can loop through to correct > the nu.mgz. > > Thanks, > Abid > > > > > > > > > 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. > > > > > -- > WARNING: E-mail sent over the Internet is not secure. Information sent by > e-mail may not remain confidential. > > DISCLAIMER: This e-mail is intended only for the individual to whom it is > addressed. It may be used only in accordance with applicable laws. If you > received this e-mail by mistake, notify the sender and destroy the e-mail > >

1 0

Qdec and one discrete variable
by ye tian 09 Aug '13

09 Aug '13

Dear freesurfers, I am experimenting qdec with one of my discrete variables. Besides qdec.table.dat file, I do have a .levels file with the two levels of the variable (say level1 and level2). However, I keep getting the following error message: Reading discrete factor levels from config file /$SUBJECTS_DIR/qdec/meditation.levels level1 done. ERROR: /$SUBJECTS_DIR/qdec/meditation.levels is invalid. Must have at least two levels. Error loading the data table. Is there something that I have missed in the declaration of the variable? Thank you very much! Sincerely, Ye

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Re: [Freesurfer] How to extract subjects' volume based on mask from spm?
by Douglas N Greve 09 Aug '13

09 Aug '13

Hi Mingxia, if you have a binarized map, then just use --id 1 with mri_cor2label (not need to for mri_binarize if it is already binary) doug On 05/21/2013 03:55 AM, zhang mingxia wrote: > Hi Doug, > > Thanks very much. A few more question after I read the description of > mri_cor2label. > > 1. there is a compulsory of mri_cor2label: --id (0-255). How can I > find the 'labelid'? > > 2. If I understand correctly, the final label will be made within > one particular 'labelid'. How if this mask is in more than one labels > (Sorry I haven't used Freesurfer for a long time, my understanding is > the labelids represent different regions. It may be wrong) ? > > 3. I have had the binarized mask created from spm, do I also need to > use mri_binarize? > > Mingxia > > > On Mon, May 20, 2013 at 6:51 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Try mri_binarize followed by mri_cor2label > doug > > > > > > On 05/20/2013 03:57 AM, zhang mingxia wrote: > > Dear Freesurfer experts, > > > > I analyzed functional data by spm and made a mask (analyze > format). I > > have also run recon-all of structural data. > > > > My question is: how to extract mean volume (from structural data) of > > the mask(from spm)? > > > > I only extracted volume(or thickness) of ROI of a label edited by > > myself and annotation file. If I can convert analyze format to a > label > > or annotation file, I can use that method. But how to convert > analyze > > format to a label or annotation? > > > > Or is there any easy way? > > > > Thanks in advance! > > > > Mingxia Zhang > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto: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. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

3 2

K2000 good for vnc?
by Jim Li 09 Aug '13

09 Aug '13

Dear Freesurfer expert, I have a simple question that I hope you can help me decide: we want to buy a Linux computer with reasonable 3D graphic card to run freesurfer. We are thinking of "NVIDIA Quadro K2000". Will that card give us problem when we run freesurfer from vnc? Thank you very much! Jim

1 0

mean thickness over hemisphere in stats file
by Mürner-Lavanchy, Ines 09 Aug '13

09 Aug '13

Dear experts, please excuse my question, I'm a beginner. I really searched for an answer in the archive, but I couldn't find out what I was doing wrong. I would like to write the mean cortical thickness of a hemisphere in the stats file. I read one can do that by using -m thickness. Where in the command line do I have to put it? I tried various versions, but it doesn't work. This would be the command: aparcstats2table --hemi rh --parc aparc --meas thickness --tablefile "directory"//"filename" --m thickness --subjects 1 2 3 4 SUBJECTS_DIR : "directory" Where do I include the -m thickness option? Or do I have to add something else? Thank you very much for your help, Ines

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 09 Aug '13

09 Aug '13

Hi David - The fact that it's taking so many tries to initialize the left ILF tells me that something has gone wrong with the data, either with the T1 to DWI registration, or with the mask, or something like that. Have you looked at any of the output files of the pre-processing? The FA map, the aparc+aseg, etc? a.y On Wed, 7 Aug 2013, Soto, David wrote: > Hi Anastasia, I checked the becs and bvals files, > there was a bug in the transposition of the columns into > 3 rows in the bvecs. But i still have problems.. > I rerun trac-all -prep and seemed fine but ended > with a Segmentation fault (core dumped) > which however is not present in the last line of the > trac-all.log (Attached). > Writing output files to /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_* > Writing spline volume to /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz > Segmentation fault (core dumped) > > Just in case I tried trac-all -bedp complains like these below, any advise appreciated, cheers - ds /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/tracula02ST.txt -bedp > INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui > INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui > Actual FREESURFER_HOME /usr/local/freesurfer > 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 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri > /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: 07 August 2013 17:22 > To: Soto, David > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] trac-all inquiry > > Hi David - Every time you run trac-all, the results get appended to this > file, so you need to look for error messages only in the more recent > invocation of trac-all. The first error there seems to be: > > Error: bvecs and bvals don't have the same number of entries > > Do you have the same number of b-values and gradient vectors and volumes > in your DWI series? > > a.y > > On Tue, 6 Aug 2013, Soto, David wrote: > >> hi >> >> I upgraded to FS 5.3 but still encountering issues with >> trac-all prep. >> >> The log is attached, things I noted after inspecting it >> >> 1) INFO: FreeSurfer build stamps do not match >> Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 >> Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 >> >> 2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb not valid >> 3) Image Exception : #22 :: ERROR: Could not open image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain >> 4) Image Exception : #22 :: ERROR: Could not open image >> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++. >> 5) ERROR: Could not read /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz >> but despite all this it says: >> trac-preproc finished without error at Tue Aug 6 21:27:30 BST 2013 >> >> thanks for your help >> >> cheers >> ds >> >> http://www1.imperial.ac.uk/medicine/people/d.soto/ >> >> >> >> >> ________________________________________ >> From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] >> Sent: 06 August 2013 19:30 >> To: Soto, David >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] trac-all inquiry >> >> I see, you're using the old version of tracula (from freesurfer 5.1). In >> that version, you had to define the number of low-b images in the >> configuration file. I strongly recommend updating to freesurfer 5.3. A lot >> of things have improved in tracula since then. >> >> Also, in the future please attach any log files as separate attachments >> instead of pasting them into the body of your email - this causes the body >> of the email to exceed the limit allowable on the list. >> >> Thanks, >> a.y >> >> >> 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. >> >> >> >>

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