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30132 discussions

FW: apply fnirt transformation on a surface
by Matt Glasser 02 Sep '13

02 Sep '13

On 9/2/13 12:02 PM, "Glasser, Matthew" <glasserm(a)wusm.wustl.edu> wrote: >Hi Bruce, > >Connectome Workbench commandline utilities can do this with FSL warp >fields: > >wb_command -surface-apply-warpfield > >One needs to use the inverse warp as the <warpfield> argument and the >forward warp as the -fnirt <forward-warp>. > >Peace, > >Matt. > >On 9/2/13 11:19 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >>A veritable game of telephone! Thanks Jesper. Matt? >> >>On Mon, 2 Sep 2013, Jesper Andersson wrote: >> >>> Hi guys, >>> I didn't think we had any tools for doing that, and said so much on the >>>FSL >>> mailbase. But apparently the WashU people has something that does just >>>that >>> for you. I think the best person to contact about the details is Matt >>> Glasser. >>> >>> J >>> >>> On 2 Sep 2013, at 15:58, Saad Jbabdi <saad(a)FMRIB.OX.AC.UK> >>> wrote: >>> >>> Hi In Probtrackx, this is done internally. >>> If you just want to transform the vertex coordinates, then I think >>> you'll need to play with the FNIRT source code - I've CC'd Jesper who >>> knows better. >>> >>> Cheers, >>> Saad >>> >>> >>> >>> On 2 Sep 2013, at 15:56, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> >>> you might check on the FSL list. I think I've seen some >>> traffic indicating that there are some tools for doing >>> this. I'l cc Saad as he might know >>> >>> cheers >>> Bruce >>> >>> >>> On Mon, 2 Sep 2013, Douglas Greve wrote: >>> >>> Hi Shani, I don't think you can apply a FNIRT >>> transform to a surface. >>> doug >>> On 9/2/13 8:20 AM, Shani Ben Amitay wrote: >>> Dear freesurfer people, >>> Any idea whether I can apply transformation >>> that was calculated by fsl >>> fnirt on the white/pial surfaces calculated >>> using the freesurfer >>> stream? >>> Thanks! >>> Shani >>> _______________________________________________ >>> 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. >>> >>> >>> >>> -- >>> Saad Jbabdi >>> University of Oxford, FMRIB Centre >>> >>> JR Hospital, Headington, OX3 9DU, UK >>> (+44)1865-222466 (fax 717) >>> www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi >>> >>> >>> >

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apply fnirt transformation on a surface
by Shani Ben Amitay 02 Sep '13

02 Sep '13

Dear freesurfer people, Any idea whether I can apply transformation that was calculated by fsl fnirt on the white/pial surfaces calculated using the freesurfer stream? Thanks! Shani

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Re: [Freesurfer] apply fnirt transformation on a surface
by Bruce Fischl 02 Sep '13

02 Sep '13

A veritable game of telephone! Thanks Jesper. Matt? On Mon, 2 Sep 2013, Jesper Andersson wrote: > Hi guys, > I didn't think we had any tools for doing that, and said so much on the FSL > mailbase. But apparently the WashU people has something that does just that > for you. I think the best person to contact about the details is Matt > Glasser. > > J > > On 2 Sep 2013, at 15:58, Saad Jbabdi <saad(a)FMRIB.OX.AC.UK> > wrote: > > Hi In Probtrackx, this is done internally. > If you just want to transform the vertex coordinates, then I think > you'll need to play with the FNIRT source code - I've CC'd Jesper who > knows better. > > Cheers, > Saad > > > > On 2 Sep 2013, at 15:56, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > > you might check on the FSL list. I think I've seen some > traffic indicating that there are some tools for doing > this. I'l cc Saad as he might know > > cheers > Bruce > > > On Mon, 2 Sep 2013, Douglas Greve wrote: > > Hi Shani, I don't think you can apply a FNIRT > transform to a surface. > doug > On 9/2/13 8:20 AM, Shani Ben Amitay wrote: > Dear freesurfer people, > Any idea whether I can apply transformation > that was calculated by fsl > fnirt on the white/pial surfaces calculated > using the freesurfer > stream? > Thanks! > Shani > _______________________________________________ > 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. > > > > -- > Saad Jbabdi > University of Oxford, FMRIB Centre > > JR Hospital, Headington, OX3 9DU, UK > (+44)1865-222466 (fax 717) > www.ndcn.ox.ac.uk/team/researchers/saad-jbabdi > > > >

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problems with aparcstats2table
by pietro de rossi 02 Sep '13

02 Sep '13

Dear FreeSurfers, I am extracting thickness values through the aparcstats2table command line. Everything works just fine for --hemi lh using the --skip flag. However, when it comes to the right hemisphere I get SUBJECTS_DIR : /usr/local/freesurfer/subjects Parsing the .stats files Traceback (most recent call last): File "/usr/local/freesurfer/bin/aparcstats2table", line 321, in <module> parc_measure_map = parsed.parse(options.meas) File "/usr/local/freesurfer/bin/fsutils.py", line 194, in parse parcid = strlist[0] IndexError: list index out of range I find it weird given that I am extracting thickness values for the same subjects. Can anybody help me find out what the problem is? Thank you in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Using edited ribbon.mgz in make_average_subject
by Miggy Chuapoco 30 Aug '13

30 Aug '13

Hi all, I've used itksnap to make edits to the ribbon.mgz (which was first converted to a nifti) file to fix the segmentations of several subjects and I now want to use this file to recreate the surface and curvature files for each subject so that I can make an average subject that uses these fixed segmentations. I am essentially trying to use a segmentation that I have fixed in itkgray to make an average subject, however looking at the processing stream in order to recreate the surface and curvature files I need to have a wm.mgz file. I've tried to find a way to maybe extract a wm.mgz file from the edited ribbon file and run -autorecon2-wm in order to recreate the surface and curvature files with the fixed segmentation, but I have yet to find a way to do this. Does anyone know if this is possible of if there is a way around this? Thanks, Miggy Chuapoco

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Longitudinal processing - Surface area
by Chung, Yoonho 30 Aug '13

30 Aug '13

Dear all, I am interested in looking at developmental changes in the brain during adolescence period in normal subjects and also comparing our controls to our clinical patients. Examples in the longitudinal processing stream tutorial have only mentioned volume and thickness, so I was wondering if area is also something we could look at and analyze. I successfully generated rate of change, spc, pc2 etc .mgz files in the post processing stage using 'long_mris_slopes' using '--meas area', but I just wanted to make sure if rate of change in surface area using freesurfer longitudinal stream is something we can report in our ms. I haven't found any papers reporting changes in the surface area using fs long stream so I was wondering if this measure is good to go or if it is something that is still work in progress Cheers, Yoon

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longitudinal norm.mgz only
by Nikhil Pratap Singh 30 Aug '13

30 Aug '13

Hi , I am new to longitudinal processing using freesurfer. I am about to process a big dataset of longitudinal images. If in the end, I am only interested in norm.mgz file, is there a way I can speed up the processing time of the entire pipeline? Since norm.mgz gets created in cross sectional processing after canorm steps of autorecon2, would these sequence of commands work for a subject? 1) recon-all -autorecon1 -subjid <tpNid> 2) recon-all -autorecon2 -subjid <tpNid> -gcareg -canorm 3) recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all 4) recon-all -long <tpNid> <templateid> -all Thanks in advance, Nikhil

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Longitudinal Processing Pipeline
by David Tate 30 Aug '13

30 Aug '13

Question regarding longitudinal processing pipeline. Is there a way to force the -long procedure to use an individual base template for a time point not used to create the base in the first place? David F. Tate, Ph.D.

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funcroi-table-sess error, "set: Variable name must begin with a letter"
by Joseph Andreano 30 Aug '13

30 Aug '13

Hi All, I'm trying to use funcroi-table-sess, but whenever I send this command: funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305 -contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat I get this error: set: Variable name must begin with a letter So far as I can tell, all the variables in that command begin with a letter. Any idea what the problem might be? _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

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error in MRI processing
by Boric, Katica A. 30 Aug '13

30 Aug '13

Hi everyone! I am new to freesurfer, and I was processing and MRI using "recon-all -autorecon1 -autorecon2 -autorecon3" command and I have a message that the processing was exited with ERRORS. When checking the recon-all. log it appears that these are the error (highlighted in yellow): #@# BA Labels lh Thu Aug 29 22:14:42 PDT 2013 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /mnt/hgfs/Linux_Share/subjects; ln -s /usr/local/freesurfer/subjects/fsaverage; cd - ln: failed to create symbolic link `./fsaverage': Operation not supported mri_label2label --srcsubject fsaverage --srclabel /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label --trgsubject MGH013_SurferOutput --trglabel ./lh.BA1.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label srclabel = /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = MGH013_SurferOutput trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/hgfs/Linux_Share/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MGH013_SurferOutput exited with ERRORS at Thu Aug 29 22:14:43 PDT 2013 If any of you could give us any advice on how to fix this we would really appreciate it! Thank you very much, Cheers, Katica

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