Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

(no subject)
by Hugh Pemberton 01 Aug '12

01 Aug '12

Hi, So when using command tkmedit *subjID* brainmask.mgz -aux -wm.mgz -surfs I receive the message: "Error: Parsing -aux option Expected an argument This option needs an argument: the image type, directory, or file name of the data to load as the aux volume." My apologies if there is an obvious answer but I can't see what is wrong (there are wm.mgz files in all subject directories), plus there doesn't seem to be anything missing as a result of this error message. Cheers for your help, Best, Hugh

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longitudinal stats
by Rajagopalan, Venkateswaran 31 Jul '12

31 Jul '12

Hi All, I am trying to do cortical thickness analysis on a single subject's longitudinal data. I am attaching the design and group.diff.mtx could any one tell me whether they are correct. Thanks venkat =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2010). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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DODS Overlay
by Ian Carroll 31 Jul '12

31 Jul '12

Hello, If I were to run a DODS -- say, an F-test looking for group differences and interactions in thickness among drug users vs non- users, dependents vs abusers, and drug use in the last month vs no use in the last month -- how would I visualize the results? I assume there's no intelligible way to make an overlay out of interactions, unless you look at the F-test output one contrast at a time (e.g., what areas show a significant interaction in thickness between dependents vs abusers and use in the last month?). Take care, Ian Carroll

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Re: [Freesurfer] Optic chiasm resisting edits
by Peter McNally 31 Jul '12

31 Jul '12

Whoops forgot to select reply all... Yes I am erasing the chiasm using tkmedit--I'll rerun autorecon-wm now and send the recon-all.log results when they finish (probably) tomorrow. Thank you, Peter On Tue, Jul 31, 2012 at 2:34 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > can you cc the list on these emails? And try rerunning autorecon2-wm and > send us the recon-all.log results? You are erasing the chiasm using > tkmedit, aren't you? > > > On Tue, 31 Jul 2012, Peter McNally wrote: > > The edits do not appear to be reflected in the filled.mgz (the chiasm is >> still present on the filled.mgz volume). The same is true for ?h.orig, and >> they are even worse than normal on ?h.orig.nofix. >> >> On Tue, Jul 31, 2012 at 2:14 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >> > >> wrote: >> hmmm. And are the edits reflected in the filled.mgz? Is the >> chiasm gone? How about in the ?h.orig and ?h.orig.nofix? >> On Tue, 31 Jul 2012, Peter McNally wrote: >> >> Hi Bruce, >> >> Thank you for your speedy response. Yes, I ran >> -autorecon2-wm -autorecon3. >> >> Best, >> Peter >> >> On Tue, Jul 31, 2012 at 2:03 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Peter >> what did you run after editing it out of the >> wm.mgz? You should >> be running -autorecon2-wm -autorecon3 >> >> cheers >> Bruce >> >> >> On Tue, 31 Jul 2012, Peter McNally wrote: >> >> Dear FreeSurfer Experts, >> >> I am using Freesurfer version 5.1 over >> at the >> University of Pennsylvania, >> and I have been running into issues with >> the optic >> chiasm. Despite having >> edited it out on both the brainmask.mgz >> and wm.mgz >> volumes, FreeSurfer has >> been insisting that it be included as a >> surface on >> multiple participants. >> Does anyone know a way to resolve this? >> Thank you >> very much for your time. >> >> Best, >> Peter McNally >> >> >> PS: I have included an example as an >> attachment >> (.pdf) >> >> >> >> >> >> >> 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<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] Recon-all -qcache curvature error & recon-all make -all
by Gibbard, Clare 31 Jul '12

31 Jul '12

Hi Bruce, Thanks, I've attached the end of the recon-all.log file for one of the subjects (the whole thing was too large). This is what I get when I run recon-all -version: $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ When I try to run recon-all -s subject_no -make all I don't think anything comes up in the log. I get this in the terminal window: clare@clare-OptiPlex-990:~/subjects$ recon-all -s subject_20 -make all Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Subject 'subject_20': make all make: Nothing to be done for `all'. clare@clare-OptiPlex-990:~/subjects$ Let me know if you need anything else. Thank you. Best wishes, Clare ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: 25 July 2012 14:44 To: Gibbard, Clare Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Recon-all -qcache curvature error & recon-all make -all Hi Clare can you send us the screen output and also what version you are running? thanks Bruce On Wed, 25 Jul 2012, Gibbard, Clare wrote: > Hello, > > I have run several scans using recon-all -all -subjid subject_no -expert > expert.opts where my expert.opts file changes the parameters for the > mri_normalize step (this works well in my scans). I then had to edit a few > of the scans by adding in more white matter and a few control points. I > re-ran them to incorporate the edits using recon-all -s subject_no -make all > -xopts-use. This worked well. > > I then ran recon-all -s subject_no -qcache ready for doing a group > analysis. I got an error reading the curvature file in those subjects I had > edited. I can see from the mailing list that others have had this error > previously and ran recon-all -s subject_no -make all to fix it. I tried > this, but I got a message saying that there was nothing to be done for all. > > Are you able to advise me on what I can try now? Do I need to go back a > step? > > Thank you very much, > Clare > > 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] Label to ROI volume
by mmoayedi＠uhnres.utoronto.ca 31 Jul '12

31 Jul '12

Dear Dr. Fischl, Thank you for your respone. What would the --reg and the --temp be in this case? Massieh > ---------------- Original message ------------------ >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >To: mmoayedi(a)uhnres.utoronto.ca-> >cc: freesurfer(a)nmr.mgh.harvard.edu-> >Subject: Re: [Freesurfer] Label to ROI volume > > try mri_label2vol (assuming by 'ROI' you mean a 3D volume) > > On Mon, 30 Jul 2012, mmoayedi(a)uhnres.utoronto.ca wrote: > > > > > Dear FS Experts, > > > > I have run recon-all on my subjects. I'm looking to convert the V1 and > various BA labels to ROIs in 3D anatomical space (orig.mgz). How would I > convert my freesufer label files to ROIs. Thank you! > > > > Massieh Moayedi > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. > >

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Optic chiasm resisting edits
by Peter McNally 31 Jul '12

31 Jul '12

Dear FreeSurfer Experts, I am using Freesurfer version 5.1 over at the University of Pennsylvania, and I have been running into issues with the optic chiasm. Despite having edited it out on both the brainmask.mgz and wm.mgz volumes, FreeSurfer has been insisting that it be included as a surface on multiple participants. Does anyone know a way to resolve this? Thank you very much for your time. Best, Peter McNally PS: I have included an example as an attachment (.pdf)

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Issues with Tracula
by Sergio Medina 31 Jul '12

31 Jul '12

Hi! First of all let me thank you for having put at our disposal such great tools as FreeSurfer and Tracula! I am trying to run Tracula on the sample data that is on the website, but I've been running into some issues. I am attaching the configuration file just in case (dmrirc_single_subject-serch). The first step "trac-all -prep" seems to run fine. The first problem comes with the second step "trac-all -bedp". The complete trace is included in the attached file 1-error-trac-all-bedp.txt After finding this on the FreeSurfer mailing list https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024042.htmlI changed the lines *${BPDIR}/fsl_sub_seychelles* for *${FSL_BIN}/fsl_sub* in the bedpostx_seychelles and I could continue, until the script seems to be stuck *Queuing parallel processing stage /volatile/tracula/results/**Diff001/dmri.bedpostX/monitor 0 slices processed 1 slices processed 1 slices processed 1 slices processed <== this line keeps on repeating* Following a suggestion I found on this other archived email http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20815.html I ran bedpostx on the dmri directory and seemed to succeed. I am attaching the output (2-bedpostx-dmri.txt). Then I tried to run trac-all -path but it stops with the following error: *niiRead(): error opening file /volatile/tracula/results/** Diff001/dmri.bedpostX/merged_**ph1samples.nii.gz ERROR: Could not read /volatile/tracula/results/** Diff001/dmri.bedpostX/merged_**ph1samples.nii.gz* I searched for that file everywhere but it doesn't exist. The closest I found was results/Diff001/dmri.bedpostX/merged_ph2samples.nii.gz Just in case I tried once again to run trac-all -bedp and this time, after having run bedpostx on the dmri directory, I get the following error (the whole output is in the attached 4-error-trac-all-bedp-2.txt file): *[...] slice 62 has already been processed slice 63 has already been processed wc: /volatile/tracula/results/**Diff001/dmri.bedpostX/**commands.txt: No such file or directory Queuing post processing stage 64 slices processed For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. kill: 390: No such process* I tried searching for a file named commands.txt but I couldn't find any. Here is the output of bugr: *FREESURFER_HOME: /i2bm/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.38-14-generic x86_64* and the output of source $FREESURFER_HOME/SetUpFreeSurfer.sh *-------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /i2bm/local/freesurfer FSFAST_HOME /i2bm/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /volatile/tracula/data/buckner_data/tutorial_subjs/ MNI_DIR /i2bm/local/freesurfer/mni FSL_DIR /usr/share/fsl/4.1* Thanks in advance for your help, any hint would be highly appreciated. Best, Sergio. -- Sergio Medina Engineer INRIA Parietal - Neurospin Bât 145, Point Courrier 156 91191 Gif/Yvette, France Tel.: (+33) 1 69 08 80 85

2 10

tracula error...
by Gonzalo Rojas Costa 31 Jul '12

31 Jul '12

Hi: I ran "trac-all -prep -c dmrirc" and it finished ok... Then, when I tried to run the command "trac-all -bedp -c dmrirc", I got the error: ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dlabel/diff/anat_brain_mask.bbr.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/nodif_brain_mask.nii.gz ln -sf /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/dwi.nii.gz /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri/data.nii.gz WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_seychelles /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri subjectdir is /usr/local/freesurfer/subjects/bmvf_23_7_2012/dmri Making bedpostx directory structure Queuing preprocessing stages [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_pre: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected Queuing parallel processing stage [: 223: NONE: unexpected operator [: 327: xbedpostx: unexpected operator [: 486: x27: unexpected operator 0 slices processed Queuing post processing stage [: 223: NONE: unexpected operator [: 314: NONE: unexpected operator [: 327: xbedpostx_post: unexpected operator [: 486: x: unexpected operator [: 486: -le: argument expected That problem occurr because my PC is not a parallelized environment?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Freesurfer GLM vs SPSS for voulme analysis
by Knut J Bjuland 31 Jul '12

31 Jul '12

Hi, I have calculated the group differences for volume using both FreeSurfer GLM and SPSS GLM. I have used gender and group as fixed factor and intercranial volume and age at MRI scan as covariate. GroupDescriptorFile 1 Title group_difference_between_group1_and_group2_gender_age DeMeanFlag 1 Class Group2Male Class Group2Female Class Group1Male Class Group1Female Variables ICU Age I used this as fsgd heading, and I used this contrast vector 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 to be able to control for gender difference and difference due to age and ICU. I get difference results between SPSS and Freesurfer. I think this is strange since I used the same data both in FreeSurfer GLM and SPSS glm. Is there anything I have done wrong? I have used both univariate and multivariate in SPSS glm. Best regards Knut J

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Freesurfer