Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

label issues (converting from the MNI space to the Talairach space)
by Qi Wu 24 Oct '13

24 Oct '13

Hi Freesurfer users, I need to design a ROI map for my project. It has to be based on certain coordinates. The ideal is to draw a circle based on the coordinates in the Talairach space in Freesurfer, which I do not know how to achieve. The alternative is to draw a spherical cluster in fsl and convert it back to the Talairach space in Freesurfer, which I don't know how to do either. Any suggestions? Many thanks Keith Postdoc fellow Toronto Western Hospital Canada

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Conversion niifty to dcm
by stdp82＠virgilio.it 24 Oct '13

24 Oct '13

Hi list, there is a way to convert niifty or .par/.rec in DICOM? Thank you very much, Stefano

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Re: [Freesurfer] skull striping error question
by Subhabrata Chaudhury 24 Oct '13

24 Oct '13

Even the Supratentorial volume ? Supratentorial volume includes some structures outside the surfaces ? Thanks Subha ----- Original Message ----- From: Bruce Fischl Sent: 10/23/13 01:13 PM To: Subhabrata Chaudhury Subject: Re: [Freesurfer] skull striping error question You should be fine if the surfaces aren't affected by the remaining skull Bruce On Wed, 23 Oct 2013, Subhabrata Chaudhury wrote: > Hi Everyone, > > I have some data where the skull striping hasnt worked properly and there are some skull remaining. > However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the > erroneous skullstriping affect the supratentorial volume estimation ? > I will be highly obliged if someone can address this concern. > > Regards > > Subha > > 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.

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Re: [Freesurfer] Problem in final analysis
by Douglas N Greve 24 Oct '13

24 Oct '13

Hi Carina, I still don't understand what you are trying to do. It looks like you have run the individual analysis (recon-all). Have you looked at the results for the individual? Do they look ok? QDEC is for group analysis, but you should make sure that the individuals look ok first doug On 10/23/2013 10:48 AM, carina(a)van-vlodrop.de wrote: > > Hi Doug, > > > maybe I created the brain correctly with the file I mentioned. > > To try if there is the problem of a wrong brain or that there is a > problem just in uploading it in qdec I heard something about an > "example-brain" from freesurfer. > > Maybe it is possible to tell me where I can find this brain to use it > for my analysis in combination with my qdec table which I can upload > without problems. > > > Carina > > > > ----- Ursprüngliche Nachricht ----- > >> Von: Douglas N Greve >> Gesendet: 21.10.13 17:13 Uhr >> An: freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] Problem in final analysis >> >> >> fsaverage is already part of the distribution. I don't understand from >> your email what the problem is. >> doug >> >> >> >> On 10/21/2013 10:03 AM, carina(a)van-vlodrop.de wrote: >> > >> > Hi Doug, >> > >> > >> > I have already run: >> > >> > >> > recon-all -s subject -qcache -target avgsubject for each subject >> > >> > >> > Is it the same file? >> > >> > I am not sure if the brain is really created or if there is a problem >> > in uploading the brain in qdec. >> > >> > Is it possible to get the fsaverage brain from freesurfer to check the >> > cause of the problem? >> > >> > >> > Thank you >> > >> > Carina >> > >> > >> > >> > >> > >> >> ----- Ursprüngliche Nachricht ----- >> >> Von: Douglas Greve >> >> Gesendet: 28.09.13 17:46 Uhr >> >> An: freesurfer(a)nmr.mgh.harvard.edu >> >> Betreff: Re: [Freesurfer] Problem in final analysis >> >> >> >> Hi Carina, run >> >> >> >> recon-all -s subject -qcache >> >> >> >> for each subject and this will create the file >> >> >> >> doug >> >> >> >> >> >> >> >> >> >> >> >> On 9/28/13 5:37 AM, carina(a)van-vlodrop.de wrote: >> >> >> >> Dear freesurfer community, we are conducting cortical-thickness >> >> analysis using freesurfer-4.4.0 and have been experiencing some >> >> problems with the final analysis steps. We are using the qdec. >> >> Uploading of the data table has been successful. When we try to >> >> use the “Analyze” command (design) in the qdec, we get the >> >> following error message: Error in Analyze: Couldn’t open file >> >> >> /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thickness.fwhm10.fsaverage.mgh >> >> Obviously, the file was never created during preprocessing. We >> >> wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and >> >> would be very grateful for your comments. Yours sincerely, Carina >> >> $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-4.4.0 Build >> >> stamp: freesurfer-Linux-centos4-stable-pub-v4.4.0 Debian version: >> >> 5.0.6 Kernel info: Linux 2.6.27.39- 1 –ql-beowulf i686 $ which >> >> surfer -> /apps/prod/i486/freesurfer-4.4.0/bin/freesurfer Used >> >> command: qdec/design/Analyze Error message: Error in Analyze: >> >> Couldn’t open file >> >> >> /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thikness.fwhm10.fsaverage.mgh >> >> >> >> >> >> >> >> _______________________________________________ Freesurfer >> >> mailing list Freesurfer(a)nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> >> > >> > >> > >> > _______________________________________________ >> > 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. >> >> -- >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> 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 >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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installation trouble - error message subjects directory not recognised
by muellersvenc 24 Oct '13

24 Oct '13

Hi all, I am running into trouble testing my freesurfer installation on a Mac (10.6.8). I followed all steps in the guide but there is something funny that freesurfer does not seem to recognise its own "subjects" directory (see attached screenshot). If screenshot is not visible, it says: -------- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING: Applications/freesurfer/subjects does not exist FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl I think it might have to do with the fact that there is a "/" missing in front of the "Applications" but I don't know where/how to change this. I checked my StartUp.csh file and there everything seems fine. However, the subjects directory was definitely created by freesurfer (also screenshot) so there is a mismatch somewhere. I am sure it is a simple thing but can someone please let me know what I should do so I can start to enjoy freesurfer? Many thanks in advance, sven

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TRACULA statistics
by Lucia Billeci 24 Oct '13

24 Oct '13

Dear all, I noticed that in the TRACULA statistics output files (pathstats.overall.txt) the variable "Count" that should indicate the number of sample paths in the WM tract is the same for all the computed tract. Could anyone tell me why this happen? Thanks a lot Regards Lucia _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa ITALY Tel: +39-0506213204 e-mail: lucia.billeci(a)ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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improvement of segmentation qualitiy by setting control points
by Annemarie Brandhofe 24 Oct '13

24 Oct '13

Dear freesurfer community, we have encountered some problems with setting control points to improve segmentation quality. Mainly, white matter was classified as grey matter after completion of the first run that incorporated control points. Now we have several questions, we would be very thankful for your comments: 1. According to your expereince, how many control points for the overall brain are usually necessary to obtain good segmentation results? 2. Are control points necessary at all? Is there a way to control the segmentation quality? 3. Is there any visual example on how to best set control points? Thank you for your help, Annemarie

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blood hyper-intensity
by Colin Reveley 24 Oct '13

24 Oct '13

Hi - I wonder if anyone has experience in dealing with T1 images where there is hyperintenisty of blood vessels? the data involved is MDEFT scans where only a head coil is used. I read it is a long solved problem for acquisition, but these scans do not correct it and nor will future scans. the difficulty is getting 3 classes (CSF,WM,GM) for nu_correct,mri_normalise or FSL Fast or whatever. It's quite a big obstacle for data that is otherwise quite excellent. One would think one could just threshold it out after brain extraction and to an extent one can but it's very imperfect. segmenting 4 classes doesn't especially work either (so far) if anyone has experience segmenting this stuff (especially getting mri_normalise to work) I'd be grateful for advice. e.g. attached Colin Reveley

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freeview "invalid drawable"
by Elissa McIntosh 24 Oct '13

24 Oct '13

Hi, When trying freeview command (see below) from the “Testing your freesurfer installation” page using my own data, freesurfer opened, but I am concerned about the “invalid drawable” lines. The message happened when I ran this command on the "bert" data too. What does invalid drawable mean? [CoS-Psychology-Murphy-iMac-QAD:/Applications/freesurfer] cmurphy% freeview -v $SUBJECTS_DIR/ABU/mri/norm.mgz -v $SUBJECTS_DIR/ABU/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/ABU/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/ABU/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/ABU/surf/rh.pial:annot=aparc:edgecolor=red 2013-10-22 12:47:02.811 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.812 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.826 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.839 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.840 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable 2013-10-22 12:47:02.853 Freeview[4214:703] invalid drawable reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Thank you, Elissa

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mri_surf2surf error - 'could not determine type of...'
by Paul Beach 23 Oct '13

23 Oct '13

Hello FS experts, I'm attempting to transform the Yeo2011 annotations (lh & rh) from fsaverage to individual subjects so as to then sample the cortical maps to subject surfaces using mri_label2vol. However, I'm getting the error in the subject line when I put in the following commands: *mri_surf2surf --srcsubject fsaverage \* *--srcsurfval lh.Yeo2011_17Networks_N1000.annot \* *--trgsubject HS_001 --trgsurfval lh.Yeo_17Network_native.annot --hemi lh* I suspected that I have to put a src_type and trg_type in there, but I wasn't sure what type of types would be appropriate for use in mri_label2vol. For the latter command I was planning on utilizing something similar to a previous e-mailer's command (below): *mri_label2vol --annot lh.Yeo2011_17Networks_N1000.HS_001.annot \* *--o outfile.nii.gz --hemi lh --subject HS_001 \* *--temp $SUBJECTS_DIR/HS_001/mri/orig.mgz --identity* Any suggestions for getting past this error? Thanks for your help, Paul -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

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Freesurfer October 2013