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ooops deleted fsaverage
by Joshua Lee 14 Dec '12

14 Dec '12

do I need to download the whole freesurfer package again to get it? - Josh

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Re: [Freesurfer] Contents of SUBJECTS_DIR
by Douglas N Greve 14 Dec '12

14 Dec '12

On 12/14/2012 04:51 PM, Tudor Popescu wrote: > Thanks Doug! I tried figuring out how to create symlinks manually (as > I think recon-all has already been run in the case of the group > analysis tutorial, therefore they were not generated automatically) > but could not find anything helpful on the wiki. cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/fsaverage > > I also looked for a tutorial on how to run recon-all on raw NIFTI > files (which I guess first have to be converted to MGZ), as I'd first > have to do this step to my own data before starting to follow the > steps described in the group analysis tutorial. You can just spec the nifti file as input (--i file.nii), you do not need to convert doug > > Tudor > > On 14 December 2012 21:23, Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Tudor, you can create a symbolic link to fsaverage rather than > copying it. > doug > > > On 12/14/2012 04:18 PM, Tudor Popescu wrote: > > Hello everyone, > > > > I'm following the group analysis tutorial, but have difficulty > getting > > all files in the right folders. I have my tutorial data set in > > //media/Dell/_FS/buckner_data// (a folder that is shared in my > > VirtualBox), and my original subjects folder in the default path of > > //home/virtualuser/freesurfer/subjects/. > > > > The tutorial page > > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data> suggests > > that the data set should be inside /$FREESURFER_HOME/subjects/, > > however I have no room in my virtual drive to copy over the > whole data > > set, and VirtualBox is making it difficult for me to extend its > size. > > I have thus defined SUBJECTS_DIR to > be//media/Dell/_FS/buckner_data//, > > but then the first command of the analysis (mris_preproc) says it > > can't find fsaverage! > > > > The command only works if I create a new folder and copy the > following > > in there: > > > > * the contents of //group_analysis_tutorial/ (i.e. folders of the > > type /004/, /008/, ..), and > > * the contents of//home/virtualuser/freesurfer/subjects/ (i.e. > > folders such as /bert/, /fsaverage/, ..) > > > > ..and then run the command from there -- however, this seems very > > cumbersome and takes a lot of time. > > > > My question: does one always have to copy the fsaverage folder > > manually at the same level as the data folders, or does it have > to be > > the other way around (i.e. data set copied into default //subjects/ > > folder)? Can't there be two environment variables, one for > fsaverages > > and one for the data set, so that no moving/copying is necessary? > > > > Many thanks for any help! > > Tudor > > > > > > _______________________________________________ > > 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 <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> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Contents of SUBJECTS_DIR
by Tudor Popescu 14 Dec '12

14 Dec '12

Hello everyone, I'm following the group analysis tutorial, but have difficulty getting all files in the right folders. I have my tutorial data set in * /media/Dell/_FS/buckner_data/* (a folder that is shared in my VirtualBox), and my original subjects folder in the default path of * /home/virtualuser/freesurfer/subjects*. The tutorial page <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data>suggests that the data set should be inside *$FREESURFER_HOME/subjects*, however I have no room in my virtual drive to copy over the whole data set, and VirtualBox is making it difficult for me to extend its size. I have thus defined SUBJECTS_DIR to be*/media/Dell/_FS/buckner_data/ *, but then the first command of the analysis (mris_preproc) says it can't find fsaverage! The command only works if I create a new folder and copy the following in there: - the contents of */group_analysis_tutorial* (i.e. folders of the type * 004*, *008*, ..), and - the contents of* /home/virtualuser/freesurfer/subjects* (i.e. folders such as *bert*, *fsaverage*, ..) ..and then run the command from there -- however, this seems very cumbersome and takes a lot of time. My question: does one always have to copy the fsaverage folder manually at the same level as the data folders, or does it have to be the other way around (i.e. data set copied into default */subjects* folder)? Can't there be two environment variables, one for fsaverages and one for the data set, so that no moving/copying is necessary? Many thanks for any help! Tudor

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Re: [Freesurfer] tksurfer - view only clusters from a certain nr of voxels
by Douglas N Greve 14 Dec '12

14 Dec '12

Hi Alex, you can't do that with tksurfer. You will have to run mri_surfcluster to create a new overlay with clusters smaller than 50 removed. doug ps. Please send emails to the FS list and not directly to me. thanks! On 12/14/2012 02:17 PM, Alex Hanganu wrote: > Dear Douglas, > > I am using tksurfer for analysing the results. > > Can you pleasetell me - what flag should I use in order to limit the > minimalthreshold of clusters to a certain number of voxels ? > For example if I want to show only those significant clusters, which > have at least 50 voxels. > > I couldn't find this answer in the wiki. > > Thanks !! > > Sincerely, > > Alex. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Beta maps
by Alex Hanganu 14 Dec '12

14 Dec '12

Dear FreeSurfer List, How can I visualise the beta maps ? previously there is a mail about this: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg02048.html The "/average7/" subject is missing in FreeSurfer 5.1, so I guess using "/fsaverage/" is the same, but that command shows no results. The command: /tksurfer fsaverage lh inflated -overlay beta.mgh -fthresh 0 /shows red areas on blue cortex. Is this correct ? Thanks, Alex.

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Registering cortical surfaces
by Patrice Koehl 13 Dec '12

13 Dec '12

Dear FreeSurfer experts, I apologize in advance if my questions seem naive or too simple: I am completely new to FreeSurfer and I am still attempting to understand how to make good use of its potential. I believe I want to use it in an unusual way. I have been given two cortical surfaces, both in the form of genus 0 triangular meshes. The two meshes are stored as OFF files, but I can easily generate other formats (PLY, OBJ, simple ASCII, ...). For both surfaces I also have informations on some sulci, in the form of list of vertices, in ASCII format. I would like to map (register) one mesh onto the other: it seems that FreeSurfer would allow me to do this with the following steps: - inflate the two surfaces - map them onto the sphere - register one surface (on the sphere) onto the second surface (on the sphere). How do I make this work? I have looked at "SurfaceRegAndTemplates", but the process described relates to specific FreeSurfer files. I will obviously need to convert my OFF files into a format that FreeSurfer can recognize, and vice versa convert the sphere representations (Source mesh, S, target mesh, T, and S on T) into an ascii format that I can analyze. Could someone give me an overview of how I should proceed, with pointers on which procedures I should use from FreeSurfer. Thanking you in advance for your help, Best regards, -Patrice

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Total brain tissue volume
by Alexopoulos, Dimitrios 13 Dec '12

13 Dec '12

Hi FS users, We've generated surfaces using FS v4.4 and would like to determine total brain tissue volume for each of our cases. Would this correspond to the 'Brain Segmentation Volume' which is standard in the output aseg.stats file. How is the 'Brain Segmentation Volume' determined, and is it different than adding up the 49 fields in the aseg.stas (subtracting out csf, ventricles, etc). What value best represents the total brain tissue volume? Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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Import % crop
by octavian lie 13 Dec '12

13 Dec '12

Dear All, Excuse the basic nature of these quetions. I coregistered 2 analyze volumes in SPM (pre and post resection MR scans for same patient) with cost function masking. I imported the preresection scan in Freesurfer, and processed it with recon -all. 1) What transform matrices should I multiply the postresection scan to get it in the FS space in alignment with the processed preresection MR, and where do I find them? 2) Once in FS, how do I crop/mask the posteresection volume using saggittal, coronal or axial planes of my choosing? (I am interested in generating a small cube containing the posteresection volume, then extracting the postresection volume itself by intensity threshold (CSF vs surronding cavity wall brain) and masking with preresection MR pial surface laterally). Please advise, Octavian.

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Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 13 Dec '12

13 Dec '12

Hi Julia, I don't think it looks terrible (unfortunately:). You might try increasing the smoothing level (maybe 10 fwhm). doug On 12/12/2012 08:02 AM, Julia Foecker wrote: > Hey Doug, > > thanks for your reply. I tried now the polar angle mapping for the left > hemisphere and I got the figure attached. > > It is difficult to see the typical polar maps in that figure and I am wondering > how to change the settings so that I will receive a typical polar angle map. > I had a 180 deg. wedge. One cycle took 38.4 sec. There were 8 cycles. The first > 5 volumes had to be deleted. I did the follwing analysis. > > mkanalysis-sess analysis rtopy.self.lh -surface self lh -TR 1.2 -retnotopy 38.4 > -fsd bold -fwhm 5 -paradigm rtopy.par -tpef tp-exclude.txt > > > Do you have any advices what to change so that it looks more like polar angle > maps? > > > Thanks so much for any further advices, > > best Julia > > > > > > On Mon, 10 Dec 2012 12:27:13 -0500 Douglas N Greve > <greve(a)nmr.mgh.harvard.edu>wrote > >> Hi Julia, that command is fine. It will not use the fieldsign or eccen. >> doug >> >> >> On 12/10/2012 10:17 AM, Julia Foecker wrote: >>> Dear Doug, >>> >>> I tried version 5 with the commands suggested on the webside and this is >>> working >>> >>> > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis) >>> . > >>> >>> However, I have only polar angle runs and I am not sure if the rtview >>> commands is only referring to polar angle maps (because the field signs are >>> included and I think that they consist of eccentricity maps as well which >>> do not have a meaning in my analysis). >>> How do I have to change the command below so that it is just referring to >>> polar maps? >>> >>> rtview --s VGP01 --lh --polar --real polar/real.nii.gz --imag >>> polar/imag.nii.gz --fsig polar/fsig.nii.gz >>> >>> >>> Many thanks for further suggestions, >>> Julia >>> >>> >>> >> -- >> 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 >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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unpacksdcmdir not working?
by thackery＠nmr.mgh.harvard.edu 13 Dec '12

13 Dec '12

Hello All, As recently as September we were downloading our fMRI scanning data from Bourget by setting the following freesurfer environment: source /usr/local/freesurfer/nmr-stable51-env and then unpacking and converting the data to Nifti format using the "unpacksdcmdir" commands: unpackscdcmdir -src "path to subject data" -targ "subject name" -scanonly "subjectname"out creating a config file, and then: unpacksdcmdir -src "path to subject data" -targ "subject name" -cfg "subjectname"config But unpackscdcmdir does not work any longer? We get the message that the command is not found. Is there a new command that must be used to perform these sorts of functions? I tried dcmunpack and it wasn't recognized either (although I may not have been using that command correctly). Thank you for any help! Sincerely, Thackery Stern Laboratory at Boston University

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