Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

update version of tksurfer and freeview
by Knut J Bjuland 17 Jan '12

17 Jan '12

Hi When I was at the Freesurfer course in December we used an updated version if Tksurfer and Freeview. Is it possible to get a download link to thesse new version of Tksurfer and Freeview please? Cheers Knut J

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Postdoc position in neuroanatomical MRI of developmental dyslexia
by Irene.Altarelli＠ens.fr 17 Jan '12

17 Jan '12

Applications are invited for a postdoc position in the team of Franck Ramus, LSCP, Institut d'Etudes Cognitives, Ecole Normale Supérieure, Paris, France. The successful candidate will investigate neuroanatomical differences between dyslexic and control children, using high-quality 3T MRI images from diffusion and T1 sequences that have already been collected as part of an imaging and genetics project. The position is available from January 1st. Candidates should have a PhD and extensive research experience in cognitive neuroscience. Expertise with the analysis of neuroanatomical images will be a strong asset. Net salary will be a minimum of 2000â¬/month and will depend on the experience of the candidate. Further details and informal enquiries may be directed to Franck Ramus (franck.ramus(a)ens.fr) Applicants should send a letter of application, clearly outlining the candidate's expertise and research interests, along with a CV, and names of 2-3 references to franck.ramus(a)ens.fr, by February 1st. The position will remain open until a suitable candidate has been found.

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control points
by Alana Shepherd 16 Jan '12

16 Jan '12

Hello, I am running version 5.0, and am finding in a few cases that some areas (most commonly STG) are missing from the original brainmask - after adding control points and re-running the pipeline, these regions are still not being picked up in the surfs or in the aseg. Can you suggest any other way of remedying this? Many thanks Alana Shepherd

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problem applying morph with mri_vol2vol
by Gregory Kirk 16 Jan '12

16 Jan '12

Hi i am trying to transform/morph a tract created with tracula into my cvs template subject space, using v.5.0 i am thinking the bb register transformation i am using is not the correct one, but it seems the logical choice, but obviously not working good as forceps minor ends up wraped around the brain stem. here is what i run mri_vol2vol --targ /study5/aa-scratch/TEENEMO/freesurfer_subjects/033/mri/norm.mgz --m3z combined_to033_elreg_afteraseg-norm.m3z --noDefM3zPath --fsl /study5/aa-scratch/TEENEMO/freesurfer_local/toot/006//dmri/xfms/diff2anat.bbr.mat --mov /study5/aa-scratch/TEENEMO/freesurfer_local/toot/006/dpath/fminor_PP_avg33_mni_bbr/path.pd.nii.gz --out ./to033path.pd.nii.gz --interp trilin --no-save-reg thanks greg

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regenerating surfs after pial edits
by Tobia, Michael 16 Jan '12

16 Jan '12

Dear Freesurfer Experts, I am trying to create surfaces that can be used in afni/SUMA for cortical based inter-subject alignment. For most of my subjects your programs have worked perfectly. But I am having a problem for two subjects with dura residual from the skull stripping that is disotrting the pial surface and produces long protruding 'handles' stemming from the cortial surface once generated in SUMA. I have made edits to the offending voxels in the brainmask.mgz using tkmedit according to the tutorial, and subsequently re-run recon-all -autorecon2-pial -autorecon3 -subjid subj05, but the surfaces still appear as they were prior to the edits. I looked at the brain.finalsurfs and noticed that the red and yellow lines demarcating WM and pial surfaces where I had deleted offending voxels remain despite re-running recon-all, as if new surfaces had not been generated. Can you tell me what I am doing wrong? Is it possible to edit the offending surface markers themselves? Any help and advice woudl be greatly appreciated. ~michael Systems Neuroscience, NIN Universitatsklinikum Hamburg-Eppendorf -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus

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question about total gray matter volume.
by Mehul Sampat 14 Jan '12

14 Jan '12

Hi Folks, I saw that mri_segstats from v5.0 onwards has an option to measure the total gray matter volume (--totalgray). My question is, If I have dataset processed with FS v4.5, can I use the mri_segstats (from v5.0) to measure the total gray matter volume on this dataset ? Thanks Mehul

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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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Freesurfer January 2012