Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Fwd: matlab: No MATLAB bin directory for this machine architecture.
by Kiley 14 Jan '12

14 Jan '12

Begin forwarded message: > From: Kiley <kiley_seymour(a)yahoo.com.au> > Date: January 13, 2012 1:17:04 PM GMT+01:00 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: matlab: No MATLAB bin directory for this machine architecture. > > Hi Freesurfers > > I have just begun using Freesurfer (and the mac terminal) to do my retinotopic mapping. So far I have found the reconstruction and pre-analysis to be far superior than anything I have used before. However, I am now at the stage of running the selxavg3-sess command ( selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ) and I am getting the following error. I googled the error and found a post that says I must change a line in the selxavg3-sess script so that my 32bit version of MATLAB can be used, but I am not very familiar with the files formats used and my attempts to change them in order to successfully progress have been futile. Your help for such a 'basic user' question will be very much appreciated. Thanks in advance! > > Kiley > > [labs-MacBook-Pro:fmri/retmapping/fsRetinotopy] kiley% selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc > > Surface data self lh > -------------------------------------------------------------- > selxavg3-sess logfile is /Users/kiley/fmri/retmapping/fsRetinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120113110658.log > -------------------------------------------------------------- > ------------------------------------------- > /Users/kiley//fmri/retmapping/fsRetinotopy/IFEE2211 > Fri Jan 13 11:06:59 CET 2012 > anadir = /Users//fmri/retmapping/fsRetinotopy/IFEE2211/bold/rtopy.self.lh > DoGLMFit = 1 > DoContrasts = 1 > UpdateNeeded = 1 > ------------------------------------------ > ------- matlab output -------------------- > > matlab: No MATLAB bin directory for this machine architecture. > > ARCH = maci64 > > ------------------------------------------ > ERROR: fast_selxavg3() failed\n

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Rerunning Freesurfer 5.1 reconall on 5.0 edited data and recreating cerebellum in brainmask
by Vy Dinh 13 Jan '12

13 Jan '12

Dear Freesurfer experts, We are about to do a mass reprocessing in our lab to update our FS 5.0 data to the FS 5.1 and would like to do the following all in one run: 1) Preserve the wm and pial edits made in the 5.0 data in 5.1 From our understanding, using the command -------------------------------------------- recon-all -all -s subjid -------------------------------------------- will preserve our (wm and pial) edits when rerunning recon-all as long as we do not use any -clear command. We've tested this command and it works. However, we would also like to (go to #2) 2) Recreate the cerebellum in brainmask while preserving our edits. We recently learned that the cerebellum should not be edited in brainmask.mgz as this would affect the volumetric measurements of this region. Since we are interested in this measurement, we want to recreate brainmask.mgz when rerunning recon-all. I came across a post that suggested adding the option -clean-bm and using brain.finalsurfs.manedit.mgz when rerunning reconall. (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg20406.html) The documentation on brain.finalsurfs.manedit.mgz suggests that this image determines the final surfaces, regardless of what brainmask.mgz looks like, which is why we could still use -cleanbm to recreate brainmask AND preserve our edits. However, when we ran the command -------------------------------------------- recon-all -all -clean-bm -s subjid (with brain.finalsurfs.manedit.mgz containing our edits in 5.0) -------------------------------------------- the edits were only preserved in one subject that we tested. The edits did not appear to be preserved at all in the other subjects. Does anyone have any explanations for why edits were preserved in this subject but not the other test subjects? Since running reconall takes a long time, we will really appreciate it if there is a way to carry over the edits we made but also recreate brainmask to get the cerebellum in one run. (Alternatively, we can add voxels back to the cerebellum, but this method would be more time consuming.) If brain.finalsurfs.manedit.mgz is indeed used to determine the final surface, would be possible to make all edits in brain.finalsurfs.manedit.mgz instead of brainmask.mgz? It seems more efficient and intuitive to make edits in one place. We would like to move forward with our reprocessing and are looking forward to your responses. Best, Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu> Vy T.U. Dinh Research Assistant, Neurological Sciences Rush University Medical Center Phone: (312) 563-3853 Fax: (312) 563-4660 Email: Vy_dinh(a)rush.edu<mailto:Vy_dinh@rush.edu>

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Re: [Freesurfer] FA and non_FA group analysis
by Douglas N Greve 13 Jan '12

13 Jan '12

If Class1>Class2, then the voxel will be red, otherwise it will be blue. Or am I misunderstanding your question? Antonella Kis wrote: > Hi Doug, > > Many thanks again for your valuable support. > > I have one more question please how I know which case I have > Class1>Class2 or Class2>Class1? > > Thanks again and have a great weekend. > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Friday, January 13, 2012 3:58 PM > *Subject:* Re: [Freesurfer] FA and non_FA group analysis > > Hi Antonelle, the way you have have it set up, C = [+1 -1] will be > positive (red) for Class1>Class2 and negative (blue) for Class2>Class1. > Your fsgd file looks ok. > > doug > > Antonella Kis wrote: > > Hi Doug and many thanks for your reply and help. If blue means neg, > > red/yellow is positive does this means that where is blue we have a > > decrease in FA for while positive means an increase? > > How I know if there is a decrease in controls versus patients and not > > opposite (FA decreases in patients versus controls)? > > > > Is my C = +1.00000 -1.00000 correct if I am interested only in group > > differences and I want to eliminate the age. > > > > Also can you please take a look on my y (please see the attached file) > > to confirm if is correct? > > > > > > Thank you very much and have a great weekend! > > Antonella > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > freesurfer > > <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Friday, January 13, 2012 2:13 PM > > *Subject:* Re: Fw: [Freesurfer] FA and non_FA group analysis > > > > Look at the original sig map. This will be signed (blue and > > red/yellow), with blue being neg, red/yellow being positive. > > doug > > > > Antonella Kis wrote: > > > Dear Doug, > > > > > > I am forwarding Bruce answer to my question since he directed me > to you. > > > > > > I need some help regarding my FA and non-FA group analysis study. I > > am not using tracula. I used the dt_recon and I have done the > > registration for my FA data on the cvs space using the > > mri_cvs_register. I used the GLM group analysis method after I > > concatenate FA from individuals into one file and used mri_glmfit-sim > > with the option grf as you recommended me some time ago: > > > > > > mri_glmfit-sim \ > > > --glmdir Group_Analysis.glmdir \ > > > --grf 2 neg \ > > > --cwpvalthresh .025 \ > > > --overwrite > > > to cache the significant clusters after multiple comparisons so I > > have the uncorrected and corrected significant map but I don't know > > how I can see if my FA is increasing or decreasing in controls > > > group versus patients group. > > > > > > I will appreciate any help/suggestion. > > > > > > Thank you. > > > Antonella > > > > > > ----- Forwarded Message ----- > > > *From:* Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> > > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>" > > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > *Sent:* Thursday, January 12, 2012 11:16 AM > > > *Subject:* Re: [Freesurfer] FA and non_FA group analysis > > > > > > Hi Antonella > > > > > > I think this is a question for Doug. > > > > > > > > > cheers > > > Bruce > > > On Thu, 12 Jan 2012, Antonella Kis > > > wrote: > > > > > > > > > > > > > > > Dear Bruce, > > > > > > > > Once again many thanks for helping.I am not using tracula. I used > > the dt_recon and I have done the registration for my FA data on the > > cvs space using the mri_cvs_register. I used the GLM group > > > > analysis method after I concatenate FA from individuals into one > > file and used > > > > > > > > > > > > mri_glmfit-sim \ > > > > --glmdir Group_Analysis.glmdir \ > > > > --grf 2 neg \ > > > > --cwpvalthresh .025 \ > > > > --overwrite > > > > > > > > to cache the significant clusters after multiple comparisons so I > > have the uncorrected and corrected significant map but I don't know > > how I can see if my FA is increasing or decreasing in controls > > > > group versus patients group. > > > > > > > > > > > > Please advise me. > > > > > > > > Thank you. > > > > Antonella > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > Phone Number: 617-724-2358 Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > > > > -- > 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 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] Fw: FA and non_FA group analysis
by Douglas N Greve 13 Jan '12

13 Jan '12

Look at the original sig map. This will be signed (blue and red/yellow), with blue being neg, red/yellow being positive. doug Antonella Kis wrote: > Dear Doug, > > I am forwarding Bruce answer to my question since he directed me to you. > > I need some help regarding my FA and non-FA group analysis study. I am > not using tracula. I used the dt_recon and I have done the > registration for my FA data on the cvs space using the > mri_cvs_register. I used the GLM group analysis method after I > concatenate FA from individuals into one file and used mri_glmfit-sim > with the option grf as you recommended me some time ago: > > mri_glmfit-sim \ > --glmdir Group_Analysis.glmdir \ > --grf 2 neg \ > --cwpvalthresh .025 \ > --overwrite > > to cache the significant clusters after multiple comparisons so I > have the uncorrected and corrected significant map but I don't know > how I can see if my FA is increasing or decreasing in controls > group versus patients group. > > > I will appreciate any help/suggestion. > > Thank you. > Antonella > > ----- Forwarded Message ----- > *From:* Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Thursday, January 12, 2012 11:16 AM > *Subject:* Re: [Freesurfer] FA and non_FA group analysis > > Hi Antonella > > I think this is a question for Doug. > > > cheers > Bruce > On Thu, 12 Jan 2012, Antonella Kis > wrote: > > > > > > > Dear Bruce, > > > > Once again many thanks for helping.I am not using tracula. I used > the dt_recon and I have done the registration for my FA data on the > cvs space using the mri_cvs_register. I used the GLM group > > analysis method after I concatenate FA from individuals into one > file and used > > > > > > mri_glmfit-sim \ > > --glmdir Group_Analysis.glmdir \ > > --grf 2 neg \ > > --cwpvalthresh .025 \ > > --overwrite > > > > to cache the significant clusters after multiple comparisons so I > have the uncorrected and corrected significant map but I don't know > how I can see if my FA is increasing or decreasing in controls > > group versus patients group. > > > > > > Please advise me. > > > > Thank you. > > Antonella > > > > > > > > > > > > > > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Selxavg3-sess Out of Memory - What are the options?
by SHAHIN NASR 13 Jan '12

13 Jan '12

Hi, I am running selxavg3-sess under freesurfer 4.5 and I faced "out of memory error" as it started "computing whitening matrices". Since they are monkey datasets, runs were relatively long (12 runs each 16 min; TR=1.4). I want to know what options do I have here? Please note that, when I applied this command to 3 runs rather than all 12 runs (by making a runlist), I didn't face this error. P.S.: I can not use version 5.1 because we don't have structural scan for this monkey and we just want to check the functional scans without any registration. I assume it is not possible in version 5. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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selxavg3-sess issue in FSFAST
by Ivan Alvarez 13 Jan '12

13 Jan '12

Dear Freesurfers, I recently attempted my first FSFAST analysis following the tutorial on http://nmr.mgh.harvard.edu/~greve/fsfast.intro.ppt <http://nmr.mgh.harvard.edu/%7Egreve/fsfast.intro.ppt> while using my own data. I stumbled across an error in selxavg3-sess which I can't decipher. The problem seems to arise when running the Matlab script fast_selxavg3.m andra returns: outtop = /media/data/analysis/FREESURFER_TEST/Project Extension format = nii.gz Error using basename Too many input arguments. Error in fast_ldanaflac (line 423) nuisregevname = basename(nuisreg,'dat'); % remove .dat Error in fast_selxavg3 (line 53) flac0 = fast_ldanaflac(analysis); I have looked through the Freesurfer documentation and mailing list but couldn't spot anyone with this issue. I am attaching the full log below, any insights would be greatly appreciated! ivan@sirsa:/media/data/analysis/FREESURFER_TEST/Project$ selxavg3-sess -sf sessid -analysis verbgen.sm5.lh Surface data fsaverage lh -------------------------------------------------------------- selxavg3-sess logfile is /media/data/analysis/FREESURFER_TEST/Project/log/selxavg3-sess-bold-verbgen.sm5.lh-120112125113.log -------------------------------------------------------------- preproc-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -a verbgen.sm5.lh -nolog -------------------------------------------------------------- preproc-sess logfile is /dev/null -------------------------------------------------------------- $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ ivan setenv FREESURFER_HOME /home/ivan/freesurfer setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 UTC 2011 x86_64 GNU/Linux /media/data/analysis/FREESURFER_TEST/Project /home/ivan/freesurfer/fsfast/bin/preproc-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -a verbgen.sm5.lh -nolog Thu Jan 12 12:51:13 GMT 2012 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain Sess01 Template ----------------------------- mktemplate-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -nolog -update Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 ---------------- Thu Jan 12 12:51:13 GMT 2012 Detected input format at nii Sess01 Update not needed Run: 001 ---------------- Thu Jan 12 12:51:13 GMT 2012 Sess01 001 Update not needed Run: 002 ---------------- Thu Jan 12 12:51:13 GMT 2012 Sess01 002 Update not needed Thu Jan 12 12:51:13 GMT 2012 mktemplate-sess completed Sess01 Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -nolog -update ------------------------------------------------ /media/data/analysis/FREESURFER_TEST/Project/Sess01 Thu Jan 12 12:51:13 GMT 2012 Sess01 Update not needed for session-level mask Sess01 Update not needed for run 001 mask Sess01 Update not needed for run 001 meanval Sess01 Update not needed for run 002 mask Sess01 Update not needed for run 002 meanval Thu Jan 12 12:51:13 GMT 2012 mkbrainmask-sess done Sess01 Registration ----------------------------- register-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 -per-run -nolog -update -------------------------------------------------------------- register-sess logfile is /dev/null -------------------------------------------------------------- Thu Jan 12 12:51:13 GMT 2012 setenv SUBJECTS_DIR /home/ivan/freesurfer/subjects cd /media/data/analysis/FREESURFER_TEST/Project /home/ivan/freesurfer/fsfast/bin/register-sess -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -dof 6 -per-run -nolog -update freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux sirsa 2.6.35-31-generic #63-Ubuntu SMP Mon Nov 28 19:29:10 UTC 2011 x86_64 GNU/Linux Session: /media/data/analysis/FREESURFER_TEST/Project/Sess01 ---------------- Thu Jan 12 12:51:13 GMT 2012 Run: 001 ---------------- Thu Jan 12 12:51:14 GMT 2012 Update not needed Run: 002 ---------------- Thu Jan 12 12:51:14 GMT 2012 Update not needed Thu Jan 12 12:51:14 GMT 2012 register-sess completed Sess01 MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -per-run -nolog -update Logfile is /dev/null ------------------------------------------- /media/data/analysis/FREESURFER_TEST/Project/Sess01 RunList: 001 002 Sess01 001 Update not needed Sess01 002 Update not needed Thu Jan 12 12:51:14 GMT 2012 mc-sess completed SUCCESSFULLY Sess01 To Surface ----------------------------- rawfunc2surf-sess -fwhm 5 -s Sess01 -d /media/data/analysis/FREESURFER_TEST/Project -fsd bold -hemi lh -nolog -update instem fmcpr outstem fmcpr.sm5.fsaverage.hemi ------------------------------ 1/1 Sess01 1/1 Sess01 001 lh --------- Thu Jan 12 12:51:14 GMT 2012 Sess01 001 Update not needed 1/1 Sess01 002 lh --------- Thu Jan 12 12:51:14 GMT 2012 Sess01 002 Update not needed Thu Jan 12 12:51:14 GMT 2012 rawfunc2surf-sess completed ---------------------------------------- Started at Thu Jan 12 12:51:13 GMT 2012 Ended at Thu Jan 12 12:51:14 GMT 2012 preproc-sess done ------------------------------------------- /media/data/analysis/FREESURFER_TEST/Project/Sess01 Thu Jan 12 12:51:14 GMT 2012 anadir = /media/data/analysis/FREESURFER_TEST/Project/Sess01/bold/verbgen.sm5.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2011 The MathWorks, Inc. R2011b (7.13.0.564) 64-bit (glnxa64) August 13, 2011 Warning: Duplicate directory name: /home/ivan/matlab. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# Sess01 ############################### /media/data/analysis/FREESURFER_TEST/Project/Sess01 ------------------------- $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ /home/ivan/freesurfer/fsfast/toolbox/fast_selxavg3.m /home/ivan/freesurfer/fsfast/toolbox/fast_ldanaflac.m /home/ivan/freesurfer/matlab/MRIread.m ------------------------- outtop = /media/data/analysis/FREESURFER_TEST/Project Extension format = nii.gz Error using basename Too many input arguments. Error in fast_ldanaflac (line 423) nuisregevname = basename(nuisreg,'dat'); % remove .dat Error in fast_selxavg3 (line 53) flac0 = fast_ldanaflac(analysis); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n -- Kind Regards, Ivan Alvarez PhD Student Imaging and Biophysics Unit UCL Institute of Child Health 30 Guildford Street, London, WC1N 1EH

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FA and non_FA group analysis
by Antonella Kis 13 Jan '12

13 Jan '12

Dear Doug, I need some help regarding my FA and non-FA group analysis study. I am not using tracula. I used the dt_recon and I have done the registration for my FA data on the cvs space using the mri_cvs_register. I used the GLM group analysis method after I concatenate FA from individuals into one file and used mri_glmfit-sim with the option grf as you recommended me some time ago: mri_glmfit-sim \ --glmdir Group_Analysis.glmdir \ --grf 2 neg \ --cwpvalthresh .025 \ --overwrite to cache the significant clusters after multiple comparisons so I have the uncorrected and corrected significant map but I don't know how I can see if my FA is increasing or decreasing in controls group versus patients group. I will appreciate any help/suggestion. Thank you. Antonella -

1 0

dcmunpack bug for unconsolidated dicoms
by Steven Lehar 13 Jan '12

13 Jan '12

There is a bug in the new *dcmunpack* that replaces the earlier * unpacksdcmdir* when it is unpacking a "fragmented" dicom directory, i.e. one in which the files were saved to DVD incrementally during the scan, as opposed to dicom files that are saved all at once, after all the scanning is complete. The difference can be seen with a 'du' command, here is a fragmented, dicom "PRL007", compared to a consolidated one "PRL007C" of the same data: $ *du* 166156 ./PRL007/DICOM/11020419/14200000 *unconsolidated* 166160 ./PRL007/DICOM/11020419 5188 ./PRL007/DICOM/11020418/50520000 207448 ./PRL007/DICOM/11020418/57160000 101648 ./PRL007/DICOM/11020418/03040000 502616 ./PRL007/DICOM/11020418/42140000 205384 ./PRL007/DICOM/11020418/17590000 1022288 ./PRL007/DICOM/11020418 1188452 ./PRL007/DICOM 1204460 ./PRL007 1022256 ./PRL007C/DICOM/11020418/03040000 *consolidated* 1022260 ./PRL007C/DICOM/11020418 1022264 ./PRL007C/DICOM 1038264 ./PRL007C When *dcmunpack* unpacks a fragmented dicom, the unpacking *appears* to succeed without errors, but the resulting f.nii file is missing a bunch of acquisitions. Calling dcmunpack on an unconsolidated and consolidated dicom respectively produces the f.nii files below: *unconsolidated*: /space/ficus/4/users/PRL_sessions/*PRL042*/prl_moco/006/f.nii $ ls -l f.nii -rw-rw-r-- 1 slehar harrisgp 125043040 Jan 6 17:04 f.nii *consolidated*: /space/ficus/4/users/PRL_sessions/*PRL042C*/prl_moco/006/f.nii $ ls -l f.nii -rw-rw-r-- 1 slehar harrisgp 201720160 Jan 11 20:48 f.nii Examination with osirix reveals the unconsolidated image to have only 318 acquisitions, the consolidated one has 513 acquisitions. And just FYI, I wrote a script called *consolidate* (see attached) that does the consolidation you see above, after which *dcmunpack* unpacked it without loss of acquisitions. This may be an issue that only affects *us* because we do very long ~20 min. functional scans with hundreds of aquisitions, people with more typical scans may not ever experience this issue, and likewise for people who save their scans all at once at the end. Steve Lehar

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manually labeled brains for segmentation atlas
by Wenger, Elisabeth 13 Jan '12

13 Jan '12

Dear Freesurfer specialists, I'm currently working on a comparison between manual segmentations and freesurfer segmentations of the hippocampus. Therefore i would be very interested in the atlas used for subcortical segmentation. On the wiki i read that the manually labeled brains used to build this atlas are about but not completely the same as the ones in the Desikan atlas, namely 39 manually labeled brains by Rahul Desikan. Could you please provide me with some rough sample descriptives on the brains used in the subcortical segmentation atlas, i.e. Age of subjects, male/female? That would be wonderful! Has this atlas changed in any way between version 4.5 and 5.1? As I am specifically working with the hippocampus segmentations, it would also be very interesting to know what the mean size of the hippocampus in this sample was – do you by any chance have some information on this? Thank you very much for your help! Cheers, Elisabeth

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[freesurfer] How do we know the size of manual drawn ROI
by zhang mingxia 12 Jan '12

12 Jan '12

Dear freesurfer experts, I have drawn a ROI manually. However, there is only vertex information (How many vertices of the ROI). How can i get the size information (mm2) of the ROI. Thank you very much Mingxia

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