Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

Imaging Genomics Post-Doctoral Fellowship
by Anderson Winkler 12 Aug '11

12 Aug '11

*Imaging Genomics Post-Doctoral Fellowship* ** A postdoctoral fellowship in Imaging Genetics at the Olin Neuropsychiatric Research Center, Institute of Living, and the Department of Psychiatry, Yale University, is currently available. The two-year NIH-funded fellowship, under the direction of Dr. David Glahn, will focus on (1) developing a deeper understanding of the genetic basis of human brain structure and function, (2) performing image analysis on large-scale imaging genomic data sets (>1000) including neuroanatomic, diffusion tensor, and resting state fMRI data, (3) developing novel image analytic approaches for gene discovery, and (4) applying imaging genomic finding and methodologies to the study of neuropsychiatric and addictive disorders. The successful candidate will have a strong methods background in imaging and/or genetics or related fields (neurogenetics, imaging, biomedical engineering, computational neuroscience) coupled with excellent writing skills. Programming experience (e.g. Matlab, shell scripting, C/C++) in Linux/Unix environments is advantageous. MDs, PhDs, or MD/PhDs are all encouraged to apply. The position can begin as early as October 1, 2011. Interested candidates are encouraged to email Dr. David Glahn (david.glahn(a)yale.edu <mailto:david.glahn@yale.edu>), including a cover letter and CV.Three letters of recommendation will be requested from qualified candidates.

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Re: [Freesurfer] Label2label on fsaverage
by Rouhollah Abdollahi 12 Aug '11

12 Aug '11

Dear Bruce I think I found the problem. The problem came from the original oriantation of T1 image and I think mris_register could not find it itself during the recon-all. I added to have initial alignment to inflated and the problem solved.( mris_register -curve -inflated ?h.sphere <template target> ?h.sphere.reg ) I think it is very important to add it to recon-all because if the user doesn't know the real oriantation it might make such a problem. Thanks for your quick response. On Thu, Aug 11, 2011 at 10:45 AM, Rouhollah Abdollahi <roohy466(a)gmail.com>wrote: > Dear Bruce > > I am working on Freesurfer 2 caret meshes. I am using > FreeSurfer2CaretConvertAndRegisterClean.sh from Van Essen lab to create > caret surfaces. when I look at my subjects' surfaces I can see in flat map > in caret some of subjects sulci patterns are really distorted and I think it > is related to sphere registration to fsaverage sphere. > Beacsue the code is using sphere.reg to create all surfaces. for the > subjects which I have less distortion on sulci pattern I have good data (3 > subjects) but for the (9 subjects) rest it seems they have problem to > register to fsaverage. Is there any way that I can be sure that > sphere.reg properly created? > > Thank you very much > > Rouhi > > > > On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Try using fsaverage as the trgsubject >> Cheers >> Bruce >> >> >> >> On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <roohy466(a)gmail.com> >> wrote: >> >> > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg >> sphere.reg --hemi rh and when I tried to load the output label file on >> fsaverage surface like inflated one it shows a lot of point looks like it is >> not deformed properly. Is it related to registration to fsaverage or >> something esle? The question is how I can register the subjects surfaces to >> fsaverage surfaces? -- With Best Regards Rouhi >> --0015175120c69a3c6804aa2ffb81 Content-Type: text/html; charset=ISO-8859-1 >> Content-Transfer-Encoding: quoted-printable Dear freesurfer experts >> > >> > I've tried to export my label file from individual space to fsaverage >> space by using this command: >> > >> > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 --trgsubject >> SUB1 --trglabel rh.V1_reg. >> > like it is not deformed properly. >> > Is it related to registration to fsaverage or something esle? >> > The question is how I can register the subjects surfaces to fsaverage >> >> >> 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. >> >> > > > -- > With Best Regards > Rouhollah Abdollahi > > > > -- With Best Regards Rouhollah Abdollahi

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QATools
by Knut J Bjuland 12 Aug '11

12 Aug '11

Hi I have looked at QAtools at https://surfer.nmr.mgh.harvard.edu/fswiki/QATools. But there seem to be some trouble. I have fixed up the wrong file issue but there is problem with my files being in the wrong order. Should I try to reorder the files to reflect the new situation or is there something wrong with my processing of recon-all. Knut J mri/transforms/talairach.xfm mri/rawavg.mgz mri/rawavg.mgz mri/orig.mgz mri/orig.mgz mri/nu.mgz mri/transforms/talairach.auto.xfm mri/transforms/talairach.auto.xfm mri/nu.mgz mri/transforms/talairach.xfm .......... ......... .......... ......... .......... ......... 14 outputfiles_NOTOK

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Tracula and number of fibres per voxel
by Jürgen Hänggi 12 Aug '11

12 Aug '11

Dear Tracula experts Is it possible to change the number of fibres per voxel in bedpostx (from 2 to 3) within the trac-all command? I did not see any option for that. Thanks in advance Cheers Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Fwd: qdec
by carolina.mr 12 Aug '11

12 Aug '11

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Error with mri_preproc
by Antonella Kis 12 Aug '11

12 Aug '11

Dear freesurfers, I am trying to see what are the group differences in cortical thickness of patients with right and left FLE compared to controls using the GLM. I created a txt file in gedit called my_age_fsgd.txt (please see the attachment) containing my subjects (patients and controls) and their age. I am not interested in doing a study versus gender just versus age. Following the instructions from the tutorial I was running the mri_preproc: mris_preproc --fsgd my_age_fsgd.txt \ --target fsaverage \ --hemi lh \ --meas thickness \ --out lh.gender_age.thickness.mgh but I got an error: ERROR: no subjects specified. Also, what should be my contrast vector if I am not interested in considering the gender. I found in one tutorial that I should create age.mat if it does not exist and it should contain this line: 0 0 1 Why this numbers? Can anyone give a hint please in how to eliminate my error and how to create the contrast vector in order to take in consideration only my subject's age? Many thanks, Antonella

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Longitudinal Subject/Base name errors
by Jeff Sadino 12 Aug '11

12 Aug '11

Hello Experts, I am using fs 5.0.0. My naming convention is similar to 100001_S01 and 100001_S02 for subject, and then 100001 for the base. Now when I process the runs longitudinally, I get: ERROR: longitudinal base ID cannot be the same as a timepoint. I believe this is because of line 4845 in recon-all: grep $longbaseid ${longbasedir}/${BaseSubjsListFname} >& /dev/null. I can just as easily cut out this part of the code, or I could manipulate the base-tps file, or rename the base folder. But I do not know if there are other spots in the code that rely on the original naming conventions. Can anyone recommend one approach over the other? Thank you very much, Jeff Sadino

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mri_glmfit with diffusion data
by Lilla Zollei 12 Aug '11

12 Aug '11

Hi, I have some diffusion scans acquired at the Childrens and when running mri_glmfit on them to reconstrct the tensors, I get the following error. "ERROR: cannot extract sDiffusion.alBValue[1] from dwi-infodump.dat" I checked the dump file and there is a field sDiffusion.alBValue[0]. Does that contain the same information? If I modify my local version of the code to read that value in, then the error message is about "ERROR: cannot extract sWiPMemBlock.alFree[8] from dwi-infodump.dat" I am not really sure how to find the correct value for that as there is nothing similar to it in the dump file. Any ideas?

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Re: [Freesurfer] FreeSurfer result wrong without error during process
by Tali Swisher 12 Aug '11

12 Aug '11

Hi all, I have a case whose resulting wmparc.mgz is completely misaligned from the brain, and is much smaller than it should be. The case ran fine, however, and I received no error messages at any point. Any ideas? Thanks! Tali On Fri, Aug 12, 2011 at 10:39 AM, Tali Swisher <tali(a)bwh.harvard.edu> wrote: > Hi all, > > I have a case whose resulting wmparc.mgz is completely misaligned from the > brain, and is much smaller than it should be. The case ran fine, however, > and I received no error messages at any point. Any ideas? I've attached the > wmparc.mgz, brain.mgz, and the recon-all.log. > > Thanks! > Tali > > > -- > Talis M. Swisher, BA > Research Assistant > Psychiatry Neuroimaging Laboratory > Harvard Medical School, Brigham and Women's Hospital > 1249 Boylston St, 3rd Floor > Boston, MA 02215 > Office: (617) 525-6119 > Cell: (336) 577-5071 > Fax: (617) 525-6150 > > -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

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Re: [Freesurfer] Label2label on fsaverage
by Rouhollah Abdollahi 12 Aug '11

12 Aug '11

Dear Bruce, I have two questions. I saw there are a lot of algorithms for mris_register. Which one are more precise and has less distortion on sulci pattern? In initial alignment if I want to rotate the surface with -rotate [ alpha is (ear to ear) beta(Back to nose) ... ]. Am I right?. and if I want that mris_register does not apply any rigid alignment after initial rotation what I have to do? Thanks Rouhi On Thu, Aug 11, 2011 at 9:25 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > What format is the attachment in? > > > > On Aug 11, 2011, at 8:32 PM, Rouhollah Abdollahi <roohy466(a)gmail.com> > wrote: > > Dear Bruce > I checked the parcellation and look quiet OK. I attached two subjects , > whcih subj_1 shows bad registration to fsaverage and subj_2 shows the good > registration. I attached a file which compare two subjects according to > sphere and sphere.reg. For the subj_1 , it has more figures to see how the > parcellation is. > Thanks in advance > > Best > Rouhi > > On Thu, Aug 11, 2011 at 10:48 AM, Bruce Fischl <<fischl(a)nmr.mgh.harvard.edu> > fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Rouhi >> >> check the parcellations. If they are correct then the sphere.reg must be >> pretty accurate. >> >> cheers >> Bruce >> >> On Thu, 11 Aug 2011, Rouhollah Abdollahi wrote: >> >> Dear Bruce >>> >>> I am working on Freesurfer 2 caret meshes. I am using ** >>> FreeSurfer2CaretConvertAndRegi**sterClean.sh from Van Essen lab to >>> create caret surfaces. when I look at my subjects' >>> surfaces I can see in flat map in caret some of subjects sulci patterns >>> are really distorted and I think it is related to sphere registration to >>> fsaverage sphere. Beacsue >>> the code is using sphere.reg to create all surfaces. for the subjects >>> which I have less distortion on sulci pattern I have good data (3 subjects) >>> but for the (9 subjects) >>> rest it seems they have problem to register to fsaverage. Is there any >>> way that I can be sure that sphere.reg properly created? >>> >>> Thank you very much >>> >>> Rouhi >>> >>> >>> >>> On Thu, Aug 11, 2011 at 4:37 AM, Bruce Fischl <<fischl(a)nmr.mgh.harvard.edu> >>> fischl(a)nmr.mgh.harvard.edu> wrote: >>> Try using fsaverage as the trgsubject >>> Cheers >>> Bruce >>> >>> >>> >>> On Aug 10, 2011, at 8:35 PM, Rouhollah Abdollahi <<roohy466(a)gmail.com> >>> roohy466(a)gmail.com> wrote: >>> >>> > .V1_reg.label --regmethod surface --srcsurfreg sphere --trgsurfreg >>> sphere.reg --hemi rh and when I tried to load the output label file on >>> fsaverage surface >>> like inflated one it shows a lot of point looks like it is not >>> deformed properly. Is it related to registration to fsaverage or something >>> esle? The question is >>> how I can register the subjects surfaces to fsaverage surfaces? -- >>> With Best Regards Rouhi --0015175120c69a3c6804aa2ffb81 Content-Type: >>> text/html; >>> charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear >>> freesurfer experts >>> > >>> > I've tried to export my label file from individual space to >>> fsaverage space by using this command: >>> > >>> > mri_label2label --srclabel rh.V1.label --srcsubject SUB1 >>> --trgsubject SUB1 --trglabel rh.V1_reg. >>> > like it is not deformed properly. >>> > Is it related to registration to fsaverage or something esle? >>> > The question is how I can register the subjects surfaces to fsaverage >>> >>> >>> 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. >>> >>> >>> >>> >>> -- >>> With Best Regards >>> Rouhollah Abdollahi >>> >>> >>> >>> >>> > > > -- > With Best Regards > Rouhollah Abdollahi > > > > <subject_1&2_side_view.odp> > > -- With Best Regards Rouhollah Abdollahi

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Freesurfer August 2011