[Freesurfer] Retinotopy stimuli
Dear freesurfers, Which stimuli do you think provide the best retinotopic maps? I have done a retinotopy analysis using the following stimuli: Polar angle: - 45 deg counter-clockwise rotating wedge - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Eccentricity: - expanding ring - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Any suggestions on how to optimize this stimulation? E.g. different period length, more runs, bi-directional, different TR Thank you! Best regards, Anders ___ Freesurfer mailing list 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.
Re: [Freesurfer] Error while loading qdec project file
Hi Nick, I have Mac OS X 10.6.7. Now I found the tmp folder, and can explain in more details what happens: As I save the Project File, the qdec_project_archive/qdec.table.dat is created, but it exists in /tmp only for several seconds and then disappears. Have you heard about something like this before? Do you know what the problem can be? Thank you, Tanja. On Wed, Jul 6, 2011 at 10:03 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: what is your operating system? linux and mac typically have a /tmp dir, unless you're running on a cluster? n. On Wed, 2011-07-06 at 15:46 +0200, Tetiana Dadakova wrote: Dear experts, When I try to load a saved Project File, I get an error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I do not have any /tmp subdirectory. Should it appear when I save the Project File? Should it be in /qdec directory? Thank you, Tanja. ___ Freesurfer mailing list 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] bbregister - Are 6 dof enough for MNI305?
Dear Freesurfers, I was wondering if you could help me clarify one question I have re the recommended use of bbregister to register PET data. If I want to register my PET data to MNI305 space used in Freesurfer, is a 6 dof rigid registration enough? I notice that the tailarach function used within autorecon1 is a 12 dof affine, so I'm guessing that bbregister is unlikely to fully register the PET data to the template space in the same way that (eg) brain.mgz is registered. Thank you very much! Best, Joao Pereira ___ Freesurfer mailing list 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.
Re: [Freesurfer] bbregister - Are 6 dof enough for MNI305?
Hi Joao You are registering to that subject's anatomicals, not a template, so 6 should be enough Cheers Bruce On Jul 7, 2011, at 6:43 AM, Joao Pereira jm...@wbic.cam.ac.uk wrote: Joao ___ Freesurfer mailing list 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.
[Freesurfer] QDEC table
Hi freesurfers Do anyone know if it's possible to automatically enter in the QDEC table the gray matter volume of every subject in the study, to avoid entering this item manually for each one ? Best regards. -- Ignacio. ___ Freesurfer mailing list 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.
[Freesurfer] freeview load fiducials from 3DSlicer
Hi guys, I've got a list of fiducials (fcsv) from 3DSlicer, Is there a way to import them within freeview? Those points look like label,x,y,z,[flag],[flag] i.e. P,57.799,-49.1799,13.07,1,1 P,-4.05607,-47.1519,8.93645,1,1 thank in advance. g. ___ Freesurfer mailing list 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.
Re: [Freesurfer] Matlab and FS
Hi Jorge, Thanks for your reply, I installed Octave in the Ubuntu machine, Should I setup something in order to use the FS commands? Best regards, Carolina 2011/7/5 jorge luis jbernal0...@yahoo.es Hi Carolina ** There is a directory freesurfer/matlab which contains several matlab-based scripts for reading and writing (after modified) surface- and volume-based data generated in freesurfer. Transport files from Linux to Windows will be tedious and things may not work properly, therefore, I recommend you to install Matlab for Linux or you can try with Octave (a kind of GNU Matlab for Linux). ** ** Cheers Jorge --- El *mar, 5/7/11, Carolina Valencia cvalen...@linkdx.com.co*escribió: De: Carolina Valencia cvalen...@linkdx.com.co Asunto: [Freesurfer] Matlab and FS Para: freesurfer@nmr.mgh.harvard.edu Fecha: martes, 5 de julio, 2011 17:39 Hello FS'users, I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, where can I find the cortical thickness in each regions (Brodmann areas, gyrus or sulci) of the brain in order to compare a normal patient with a patiwnt who has a cortical dysplasia ? Thanks a lot for your help, Carolina -Adjunto en línea a continuación- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduhttp://es.mc247.mail.yahoo.com/mc/compose?to=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. -- -- *Carolina Valencia Muñoz* Bioingeniera *LINK DIAGNOSTICO DIGITAL SA *Cel: 3016411824 Of: (4) 444 54 65 ___ Freesurfer mailing list 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.
[Freesurfer] cortical dysplasia
Hello FSexperts I have a MPRAGE image of cortical dysplasia, I have some regions of grey matter within the white matter, and I measured the cortical thickness in the projections of those regions and I expected to find a thinnercortex instead I found a cortical thickening. FS takes into account the embedded region of the grey matter to measure the cortical thickness? Best regards, Carolina ___ Freesurfer mailing list 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.
Re: [Freesurfer] cortical dysplasia
Carolina, We have worked with several cases of MCD (including cortical dysplasia). We have published this paper: https://surfer.nmr.mgh.harvard.edu/pub/articles/jon_372_LR.pdf It may help. But in most cases of cortical dysplasia (not Gray matter heterotopia cases) you'll find a ticker cortex not a thinner one. But maybe you could post one image illustrate this problem. PPJ On Thu, Jul 7, 2011 at 10:39, Carolina Valencia cvalen...@linkdx.com.cowrote: Hello FSexperts I have a MPRAGE image of cortical dysplasia, I have some regions of grey matter within the white matter, and I measured the cortical thickness in the projections of those regions and I expected to find a thinnercortex instead I found a cortical thickening. FS takes into account the embedded region of the grey matter to measure the cortical thickness? Best regards, Carolina ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
Re: [Freesurfer] bbregister - Are 6 dof enough for MNI305?
The conversion from PET to MNI305 uses two registration steps. One from PET to anatomical, one from anat to mni305. bbregister handles the first one, so 6 dof is fine. doug Joao Pereira wrote: Dear Freesurfers, I was wondering if you could help me clarify one question I have re the recommended use of bbregister to register PET data. If I want to register my PET data to MNI305 space used in Freesurfer, is a 6 dof rigid registration enough? I notice that the tailarach function used within autorecon1 is a 12 dof affine, so I'm guessing that bbregister is unlikely to fully register the PET data to the template space in the same way that (eg) brain.mgz is registered. Thank you very much! Best, Joao Pereira ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] matlab loading problem (mkcontrast, selxavg3-sess)
Hi Paola, I can't tell from the output what went wrong. One thing that may be going wrong is that you might not have the matlab binary in your path. From a terminal, type 'which matlab' (no quotes). Also, please don't send logs and error messages in rtf or doc formats -- it makes it harder for us to read! thanks doug Paola Binda wrote: Hi all I'm having trouble with the interface between freesurfer and matlab too in my case, running mkcontrast does not open matlab and eventually generates an error Any help to work around this problem would be very much appreciated I'm running freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on a Mac OS X 10.6.8 (please see details of the system/command/error message in the rtf file in attach) I've just installed Freesurfer and this is the first time I try this command Paola What is your platform and what version of FS are you using? doug On 12/15/10 2:42 PM, Katherine Sledge Moore wrote: I am having trouble with the interface between freesurfer and matlab. When I run mkcontrast-sess and selxavg3-sess, matlab opens, but nothing happens (the script does not finish.) When I force it to quit, I get the error -display: Command not found. In both mkcontrast and selxavg3-sess, the command to call matlab is something along the lines of matlab -display iconic. Any thoughts as to why the -display iconic part is not being interpreted? Katherine Sledge Moore Postdoctoral Associate Visual Cognitive Neuroscience Laboratory Yale University http://camplab.psych.yale.edu/ http://pantheon.yale.edu/~khs8 http://pantheon.yale.edu/%7Ekhs8 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Viewing a multi-frame image?
Dear all, I created a 3-frame image using a command similar to: mris_preproc --target fsaverage --hemi lh --fwhm 5 \ --out xrun/lh.cope1.mgh \ --iv fbert1.feat/stats/cope1.nii.gz fbert1.feat/reg/freesurfer/anat2exf.register.dat \ --iv fbert2.feat/stats/cope1.nii.gz fbert2.feat/reg/freesurfer/anat2exf.register.dat How can I view all 3 frames of the lh.cope1.mgh? I see just one frame with: tksurfer fsaverage lh inflated -overlay xrun/lh.cope1.mgh And don't know how to toggle between the frames. Thank you for your help! Cheers, Aga ___ Freesurfer mailing list 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.
Re: [Freesurfer] Viewing a multi-frame image?
Hi Aga, try View-Configure-Overlay. The config window will have a time point entry at the top. doug Agnieszka Burzynska wrote: Dear all, I created a 3-frame image using a command similar to: mris_preproc --target fsaverage --hemi lh --fwhm 5 \ --out xrun/lh.cope1.mgh \ --iv fbert1.feat/stats/cope1.nii.gz fbert1.feat/reg/freesurfer/anat2exf.register.dat \ --iv fbert2.feat/stats/cope1.nii.gz fbert2.feat/reg/freesurfer/anat2exf.register.dat How can I view all 3 frames of the lh.cope1.mgh? I see just one frame with: tksurfer fsaverage lh inflated -overlay xrun/lh.cope1.mgh And don't know how to toggle between the frames. Thank you for your help! Cheers, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
[Freesurfer] make_average_subject error
Hi all Could anyone help me with this error: MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 i=5A595959, in_array_size=133467 annot file: /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot This appeared after trying to average my subject data. It says ' vertex index out of range '. All acquisitions were made using the same parameters so I don't know what this may mean. Thanks in advance -- Leo Kay. ___ Freesurfer mailing list 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.
Re: [Freesurfer] Viewing a multi-frame image?
Dear Doug, Yes, it works, thank you so much! Cheers, Aga On 7/7/11 3:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Aga, try View-Configure-Overlay. The config window will have a time point entry at the top. doug Agnieszka Burzynska wrote: Dear all, I created a 3-frame image using a command similar to: mris_preproc --target fsaverage --hemi lh --fwhm 5 \ --out xrun/lh.cope1.mgh \ --iv fbert1.feat/stats/cope1.nii.gz fbert1.feat/reg/freesurfer/anat2exf.register.dat \ --iv fbert2.feat/stats/cope1.nii.gz fbert2.feat/reg/freesurfer/anat2exf.register.dat How can I view all 3 frames of the lh.cope1.mgh? I see just one frame with: tksurfer fsaverage lh inflated -overlay xrun/lh.cope1.mgh And don't know how to toggle between the frames. Thank you for your help! Cheers, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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.
Re: [Freesurfer] make_average_subject error
Hi Leo, check to see if that subject's analysis is up-to-date. This usually happens when it was only partially re-run. doug leonardo kay wrote: Hi all Could anyone help me with this error: MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 i=5A595959, in_array_size=133467 annot file: /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot This appeared after trying to average my subject data. It says ' vertex index out of range '. All acquisitions were made using the same parameters so I don't know what this may mean. Thanks in advance -- Leo Kay. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] more on fieldsign problems-
Hi Michelle, do the eccen and polar maps look ok? Also, I would probably smooth them a little bit. The field sign calculation is basically a spatial derivative so it can be sensitive to noise. doug Michelle Umali wrote: Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors: 1) ran recon-all -all 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d rh.occip.patch.flat 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 paradigm rtopy.par -nskip 4 fwhm 0 5) selxavg3-sess -a rtopy.self.rh -s sj09 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09 When I looked at the fieldsign map using: 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign all I got were blue and red speckles. The polar and eccentricity maps seemed ok. Any help would be great. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] QDEC table
the 'generate stats data tables' button in the Subjects tab will do
this. see the section 'Stats Data Import' in the tutorial:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis
which is copied here:
It is possible to import the aseg and aparc data from the
FreeSurfer-processed group data. To do so, press the 'Generate Stats
Data Tables' button. This will run the FreeSurfer utilities
asegstats2table and aparcstats2table on your group data. Upon
completion (you should see the progress in the terminal screen), then
the 'Generate Stats Data Tables' button becomes a menu-selection list.
Within that menu, you can select 'aseg.volume'. Upon doing so, the
volumetric data for various subcortical structures are displayed. You
could choose for example 'Left-Lateral-Ventricle', then click 'Add
Selection to Data Table'. Upon doing so, it will appear in the
'Discrete and Continuous Factors' display of the 'Data Table View'.
'Left-Lateral-Ventricle' is now available as a possible factor in your
analysis ('Left-Hippocampus' and 'Right-Hippocampus' were imported
from aseg.volume in this manner). If you select
'Left-Lateral-Ventricle' in the 'Data Table View', then the volumetric
data for all the subjects is plotted. You can look for patterns or
outliers. If you suspect an outlier, right-click on that point in the
scatter-plot. You can then either exclude that subject, or examine it
in tkmedit or tksurfer, to check for possible problems in the original
scan data. Lastly, you can save this newly imported data (in this
case, 'Left-Lateral-Ventricle') to your qdec.table.dat file by
selecting 'Save Data Table' from the File menu (but dont do this for
the tutorial).
n.
On Thu, 2011-07-07 at 09:18 -0400, Ignacio Letelier wrote:
Hi freesurfers
Do anyone know if it's possible to automatically enter in the QDEC
table the gray matter volume of every subject in the study, to avoid
entering this item manually for each one ?
Best regards.
--
Ignacio.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
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.
[Freesurfer] DOF and smoothing in mri_glmfit
Dear all, I am combining 3 runs of a subject using fixed effects GLM and I wanted to make sure I am doing the right thing. For each subject I use: mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 , while lh.cope1.mgh contains the concatenated cope1 images of the same subject in fsaverage space (the same for varcope1). 1) Is it the right way? 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it correct? 3) The functional data has not been smoothed in the 1st level analysis in FSL (as recommended), and also not smoothed during sampling the copes to a common space. Therefore I want to smooth it here for the first time, but only with 5mm. Does it sound right? Cheers, Aga ___ Freesurfer mailing list 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.
Re: [Freesurfer] DOF and smoothing in mri_glmfit
Hi Aga, your commands look right. For the DOF, it should be the sum of the DOFs from all the runs (probably won't make much of a difference). Smoothing is a bit of an issue when you want to look at individual results. Technically, you should smooth before you do the first level analysis (ie, before your compute the varcope), but this would require doing the FEAT analysis directly on surface data. Smoothing after computing the varcope means that the varcope will not be accurate (it will be too large). The penalty is that you will see less activation than you should. At the group level, this is not such a big deal because you're either not using the varcope or you are using it as a weight. doug Agnieszka Burzynska wrote: Dear all, I am combining 3 runs of a subject using fixed effects GLM and I wanted to make sure I am doing the right thing. For each subject I use: mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 , while lh.cope1.mgh contains the concatenated cope1 images of the same subject in fsaverage space (the same for varcope1). 1) Is it the right way? 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it correct? 3) The functional data has not been smoothed in the 1st level analysis in FSL (as recommended), and also not smoothed during sampling the copes to a common space. Therefore I want to smooth it here for the first time, but only with 5mm. Does it sound right? Cheers, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] DOF and smoothing in mri_glmfit
Dear Doug, Thank you so much. I completely see you point, but I have re-run the 1st level feat without smoothing just because it has been recommended not to smooth in the volume and then transfer it onto the surface, but rather first smooth on the surface (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). What I plan to do in the end is to include the cortical thickness as the vertex-wise covariate in the functional group analysis. So the final analysis will be on the group level, where, as you say, the varcopes should not matter that much. However, I was also thinking of analyzing varcopes in addition to copes (group analysis) to relate the variance of BOLD signal to the thickness. Would you then recommend going back and taking the initial 1st level analysis with regular smoothing? Thank you! Aga On 7/7/11 4:43 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Aga, your commands look right. For the DOF, it should be the sum of the DOFs from all the runs (probably won't make much of a difference). Smoothing is a bit of an issue when you want to look at individual results. Technically, you should smooth before you do the first level analysis (ie, before your compute the varcope), but this would require doing the FEAT analysis directly on surface data. Smoothing after computing the varcope means that the varcope will not be accurate (it will be too large). The penalty is that you will see less activation than you should. At the group level, this is not such a big deal because you're either not using the varcope or you are using it as a weight. doug Agnieszka Burzynska wrote: Dear all, I am combining 3 runs of a subject using fixed effects GLM and I wanted to make sure I am doing the right thing. For each subject I use: mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 , while lh.cope1.mgh contains the concatenated cope1 images of the same subject in fsaverage space (the same for varcope1). 1) Is it the right way? 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it correct? 3) The functional data has not been smoothed in the 1st level analysis in FSL (as recommended), and also not smoothed during sampling the copes to a common space. Therefore I want to smooth it here for the first time, but only with 5mm. Does it sound right? Cheers, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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.
Re: [Freesurfer] Retinotopy stimuli
I'd also be very interested to hear about good reinotopic stimuli; we've used 6Hz and 14 ring sizes for eccentricity mapping in the past. Thomas Ballinger On Thu, Jul 7, 2011 at 3:56 AM, Anders Hougaard ahouga...@dadlnet.dkwrote: Dear freesurfers, Which stimuli do you think provide the best retinotopic maps? I have done a retinotopy analysis using the following stimuli: Polar angle: - 45 deg counter-clockwise rotating wedge - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Eccentricity: - expanding ring - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Any suggestions on how to optimize this stimulation? E.g. different period length, more runs, bi-directional, different TR Thank you! Best regards, Anders ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
Re: [Freesurfer] DOF and smoothing in mri_glmfit
The problem with doing the smoothing at the first level in FEAT is that it will be volume-based, not surface-based. I'm not sure what to tell you about using the varcopes. They will certainly be very noisy without smoothing, so probably smoothing is a good idea, even if it's volume-based. doug Agnieszka Burzynska wrote: Dear Doug, Thank you so much. I completely see you point, but I have re-run the 1st level feat without smoothing just because it has been recommended not to smooth in the volume and then transfer it onto the surface, but rather first smooth on the surface (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). What I plan to do in the end is to include the cortical thickness as the vertex-wise covariate in the functional group analysis. So the final analysis will be on the group level, where, as you say, the varcopes should not matter that much. However, I was also thinking of analyzing varcopes in addition to copes (group analysis) to relate the variance of BOLD signal to the thickness. Would you then recommend going back and taking the initial 1st level analysis with regular smoothing? Thank you! Aga On 7/7/11 4:43 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Aga, your commands look right. For the DOF, it should be the sum of the DOFs from all the runs (probably won't make much of a difference). Smoothing is a bit of an issue when you want to look at individual results. Technically, you should smooth before you do the first level analysis (ie, before your compute the varcope), but this would require doing the FEAT analysis directly on surface data. Smoothing after computing the varcope means that the varcope will not be accurate (it will be too large). The penalty is that you will see less activation than you should. At the group level, this is not such a big deal because you're either not using the varcope or you are using it as a weight. doug Agnieszka Burzynska wrote: Dear all, I am combining 3 runs of a subject using fixed effects GLM and I wanted to make sure I am doing the right thing. For each subject I use: mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 , while lh.cope1.mgh contains the concatenated cope1 images of the same subject in fsaverage space (the same for varcope1). 1) Is it the right way? 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it correct? 3) The functional data has not been smoothed in the 1st level analysis in FSL (as recommended), and also not smoothed during sampling the copes to a common space. Therefore I want to smooth it here for the first time, but only with 5mm. Does it sound right? Cheers, Aga ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] tracula bvecs problem
Great, good to know. My LANG is en_US.UTF-8, everything else is not set. On Thu, 7 Jul 2011, Franz Liem wrote: Dear Anastasia all. I fixed it. The problem was my LOCALE setting which leads to different handling of decimal separators by awk (for further details see http://objectmix.com/awk/716715-awk-different-decimal-separator-different-linux-distros.html). My original setting was: % locale LANG=de_CH.UTF-8 LC_COLLATE=de_CH.UTF-8 LC_CTYPE=de_CH.UTF-8 LC_MESSAGES=de_CH.UTF-8 LC_MONETARY=de_CH.UTF-8 LC_NUMERIC=de_CH.UTF-8 LC_TIME=de_CH.UTF-8 LC_ALL= Therefore awk used the comma as decimal separator. In order to change this I added the following line to the .tcshrc file: setenv LC_ALL en_US resulting in: % locale LANG=de_CH.UTF-8 LC_COLLATE=en_US LC_CTYPE=en_US LC_MESSAGES=en_US LC_MONETARY=en_US LC_NUMERIC=en_US LC_TIME=en_US LC_ALL=en_US Now the bvec rotation and correction works fine. Is your setting en_US or another format (e.g. en_US.ISO8859-1, en_US.ISO8859-15, en_US.US-ASCII, en_US.UTF-8)? Anastasia and Priti, thank you for your time. Best, Franz Am 06.07.2011 um 21:32 schrieb Anastasia Yendiki: I'm attaching what I get when I run it. Only the trailing zeros are missing. On Wed, 6 Jul 2011, Franz Liem wrote: If i flip4fsl my fake file the the numbers after the decimal point are missing in the output (bvecs_bvecs_onezero3decpoint1_western_out). I have attached a fake bvecs fitting your tutorial data (70 lines). Would you be so kind, as to run this. Thank you so much for your help, Franz new1.mghdti.bvecs___ Freesurfer mailing list 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Retinotopy stimuli
hi anders, the optimal set of stimulus parameters will depend somewhat on what cortical area(s) you are trying to map and on the details of your acquisition. in general, stimulating with both clockwise- and counterclockwise-rotating wedges for polar angle mapping and with both expanding and contracting rings for eccentricity mapping improves the accuracy of the maps, and the proper analysis of this data is implemented fsfast. the width of the wedge or the ring will depend on the cortical area you are trying to stimulate, but you may want to consider a thinner wedge. also, 8 Hz flickering has been shown to activate area V1 more strongly than other frequencies, and smoothly moving stimuli can also help. then, depending on your voxel size, field strength, coil array, etc., you could include more cycles and may need to average together multiple runs. marty, roger et al. have a few nice papers that i'd recommend that discuss some of these details relating to phase-encoded retinotopic stimuli. Sereno Tootell. Curr Opin Neurobiol. 2005;15(2):135-44. Tootell et al. J Neurosci. 1997;17(18):7060-78. Sereno et al. Science. 1995;268(5212):889-93. (the '97 paper discusses the ring/wedge thickness, the '95 paper discusses the advantages of using both expanding + contracting stimuli, and the '05 paper discusses the use of smoothly varying stimuli.) hope this helps. were you able to get reasonable looking maps with the stimuli you described below? -jon On Thu, 7 Jul 2011, Anders Hougaard wrote: Dear freesurfers, Which stimuli do you think provide the best retinotopic maps? I have done a retinotopy analysis using the following stimuli: Polar angle: - 45 deg counter-clockwise rotating wedge - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Eccentricity: - expanding ring - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Any suggestions on how to optimize this stimulation? E.g. different period length, more runs, bi-directional, different TR Thank you! Best regards, Anders ___ Freesurfer mailing list 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.
Re: [Freesurfer] Retinotopy stimuli
Hi Anders, I agree with the points Jon made. 8 Hz flicker is also what I use. I haven't tried lower frequencies, but I think you would definitely have reduced SNR if you did. I also use rather thin wedges and rings and smoothly vary their position. I would add that a longer cycle duration (e.g. 64 seconds) seems to provide better phase estimates. I had been using a shorter duration (32 seconds) for awhile, and while you can get reasonable results (and better SNR because of more cycles/scan), I was also noticing irregularities in the maps (e.g. spots of upper field preference where it should be lower field). When I did a direct comparison between the two cycle durations, the maps looked much cleaner with the longer cycle. Because the data can be rather noisy (regardless of field strength), multiple scans are important. I use 4 scans for polar angle (2 CW, 2 CCW) and 2 for eccentricity (1 expanding, 1 contracting), although I would do more in a session if I thought the typical subject could stand it. My current settings are 5 cycles/scan, 64 second cycle duration, 128 TRs, TR = 2.5 sec, so ~5.5 minutes / scan. A 3 sec TR would work fine too, and allow for 6 cycles/scan, which would improve SNR (and increase total scan duration). Don Date: Thu, 7 Jul 2011 11:30:13 -0400 From: j...@nmr.mgh.harvard.edu To: ahouga...@dadlnet.dk CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Retinotopy stimuli hi anders, the optimal set of stimulus parameters will depend somewhat on what cortical area(s) you are trying to map and on the details of your acquisition. in general, stimulating with both clockwise- and counterclockwise-rotating wedges for polar angle mapping and with both expanding and contracting rings for eccentricity mapping improves the accuracy of the maps, and the proper analysis of this data is implemented fsfast. the width of the wedge or the ring will depend on the cortical area you are trying to stimulate, but you may want to consider a thinner wedge. also, 8 Hz flickering has been shown to activate area V1 more strongly than other frequencies, and smoothly moving stimuli can also help. then, depending on your voxel size, field strength, coil array, etc., you could include more cycles and may need to average together multiple runs. marty, roger et al. have a few nice papers that i'd recommend that discuss some of these details relating to phase-encoded retinotopic stimuli. Sereno Tootell. Curr Opin Neurobiol. 2005;15(2):135-44. Tootell et al. J Neurosci. 1997;17(18):7060-78. Sereno et al. Science. 1995;268(5212):889-93. (the '97 paper discusses the ring/wedge thickness, the '95 paper discusses the advantages of using both expanding + contracting stimuli, and the '05 paper discusses the use of smoothly varying stimuli.) hope this helps. were you able to get reasonable looking maps with the stimuli you described below? -jon On Thu, 7 Jul 2011, Anders Hougaard wrote: Dear freesurfers, Which stimuli do you think provide the best retinotopic maps? I have done a retinotopy analysis using the following stimuli: Polar angle: - 45 deg counter-clockwise rotating wedge - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Eccentricity: - expanding ring - 8 unique positions - flickering at 2 Hz - stimulation period: 36 sec - no. of cycles: 6 - TR = 3 Any suggestions on how to optimize this stimulation? E.g. different period length, more runs, bi-directional, different TR Thank you! Best regards, Anders ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
[Freesurfer] talaraich ERROR
Hi FSexperts, I have a case of a child with *Hydrocephalus and cortical dysplasia, the patient has a subcutaneous ventriculo-peritoneal shunt that produces an artifice in all MRI sequences, I try to recon-all but it exit with ERROR* # #@# Talairach Failure Detection Thu Jul 7 11:03:21 COT 2011 /home/cvalencia/freesurfer/subjects/volumetria/hptu_vol04/hptu_vol04/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Linux cvalencia-Precision-WorkStation-T3400 2.6.35-30-generic-pae #54-Ubuntu SMP Tue Jun 7 20:28:33 UTC 2011 i686 GNU/Linux recon-all -s hptu_vol04 exited with ERRORS at Thu Jul 7 11:03:21 COT 2011 is possible to process it in automated fashion? Thanks, Best regards, Carolina ___ Freesurfer mailing list 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.
Re: [Freesurfer] Matlab and FS {Disarmed}
Hi Carolina You simply need to add the path ‘your FS installation dir/freesurfer/matlab’ to the search path in Octave: addpath(‘your FS installation dir/freesurfer/matlab’); For example, to build a histogram of cortical thickness values for the first subject of your study, you can try: thickness_data = squeeze(load_mgh(‘lh.thickness.mgh’)); hist(thickness_data(:,1)); where lh.thickness.mgh contains the thickness data for the left hemisphere of your subjects (eg.. those generated with mris_preproc) Cheers Jorge --- El jue, 7/7/11, Carolina Valencia cvalen...@linkdx.com.co escribió: De: Carolina Valencia cvalen...@linkdx.com.co Asunto: Re: [Freesurfer] Matlab and FS Para: jorge luis jbernal0...@yahoo.es CC: freesurfer@nmr.mgh.harvard.edu Fecha: jueves, 7 de julio, 2011 15:30 Hi Jorge, Thanks for your reply, I installed Octave in the Ubuntu machine, Should I setup something in order to use the FS commands? Best regards, Carolina 2011/7/5 jorge luis jbernal0...@yahoo.es Hi Carolina There is a directory freesurfer/matlab which contains several matlab-based scripts for reading and writing (after modified) surface- and volume-based data generated in freesurfer. Transport files from Linux to Windows will be tedious and things may not work properly, therefore, I recommend you to install Matlab for Linux or you can try with Octave (a kind of GNU Matlab for Linux). Cheers Jorge --- El mar, 5/7/11, Carolina Valencia cvalen...@linkdx.com.co escribió: De: Carolina Valencia cvalen...@linkdx.com.co Asunto: [Freesurfer] Matlab and FS Para: freesurfer@nmr.mgh.harvard.edu Fecha: martes, 5 de julio, 2011 17:39 Hello FS'users, I'm trying to do an histogram of cortical thickness for 2 cases in matlab, but the problem is that I have Installed matlab in a computer (windows) and FS in another one (ubuntu) Can I configure something to use the FS commands in matlab in order to obtain some graphs? And also, where can I find the cortical thickness in each regions (Brodmann areas, gyrus or sulci) of the brain in order to compare a normal patient with a patiwnt who has a cortical dysplasia ? Thanks a lot for your help, Carolina -Adjunto en línea a continuación- ___ Freesurfer mailing list 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. -- -- Carolina Valencia Muñoz Bioingeniera LINK DIAGNOSTICO DIGITAL SA Cel: 3016411824 Of: (4) 444 54 65 -Adjunto en línea a continuación- ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
Re: [Freesurfer] talaraich ERROR
Yep, use tkregister2 --s subject --fstal there are instructions in the trouble shooting tutorial on the wiki. doug Carolina Valencia wrote: Hi FSexperts, I have a case of a child with /Hydrocephalus and cortical dysplasia, the patient has a subcutaneous ventriculo-peritoneal shunt that produces an artifice in all MRI sequences, I try to recon-all but it exit with ERROR/ # #@# Talairach Failure Detection Thu Jul 7 11:03:21 COT 2011 /home/cvalencia/freesurfer/subjects/volumetria/hptu_vol04/hptu_vol04/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0., pval=0. threshold=0.0050) Linux cvalencia-Precision-WorkStation-T3400 2.6.35-30-generic-pae #54-Ubuntu SMP Tue Jun 7 20:28:33 UTC 2011 i686 GNU/Linux recon-all -s hptu_vol04 exited with ERRORS at Thu Jul 7 11:03:21 COT 2011 is possible to process it in automated fashion? Thanks, Best regards, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] Error with Tksurfer
Hi Antonella, did bert inflated look ok on the other computer? Usually this problem goes away if you update the video card driver. cheers Bruce On Thu, 7 Jul 2011, Antonella Kis wrote: Good afternoon Bruce, I am still trying to fix my error related to the surface image display when using tksurfer bert lh inflated. As you saw the image looks weird and what I in the mean time I tried something: I save the weird surface displayed by that computer using SAVE SURFACE AS and I transfers this file nsmed by me lh.bertsurf to another computer. When I looked on the image using tksurfer bert lh bertsurf, the surface that came up was exactly like the bert lh inflated should be, having the same number of vertices and faces. Can you or somebody else give me some advice on what to do so I can get the same display on the other computer? Seems that everything is well calculated just the surface display/image is looking weird on that computer. What can be the problem? I attached the saved surface from the computer where it looked weird so the called weird surface. Also can I save a surface and loaded in freesurfer but not as a tiff image? What's the best way to save my volumes and/or surfaces? Thank you very much for your help. Antonella ___ Freesurfer mailing list 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.
[Freesurfer] preprocessing qc
Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 ___ Freesurfer mailing list 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.
Re: [Freesurfer] more on fieldsign problems-
Hi Doug, The eccen and polar maps look ok, although activation tends to be limited to the occipital poles and lateral surface not really along the calcarine. Is it possible to find out how the colors in the eccen and polar images correspond to positions in the stimulus using rtview? There's no legend. Thanks. Michelle Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: Hi Michelle, do the eccen and polar maps look ok? Also, I would probably smooth them a little bit. The field sign calculation is basically a spatial derivative so it can be sensitive to noise. doug Michelle Umali wrote: Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors: 1) ran recon-all -all 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d rh.occip.patch.flat 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 paradigm rtopy.par -nskip 4 fwhm 0 5) selxavg3-sess -a rtopy.self.rh -s sj09 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09 When I looked at the fieldsign map using: 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign all I got were blue and red speckles. The polar and eccentricity maps seemed ok. Any help would be great. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] QC Montages error
I am getting an error when using a script that combines these 3 actions: preproc.sh std_map_qc_montages.bash put_tpef.bash Freesurfer version 4 SUBJECTS_DIR: /cluster/manoach/AS/RespMon12C/subjects Script: /cluster/manoach/AS/RespMon12C/scripts/preproc_std_qc_montages_put_tpef.sh It looks like the preproc-sess finishes okay, but the problem starts afterwards, but I'm not sure how to fix this easily.. it looks like it's looking for files that aren't there, but I haven't gotten this error before. Thanks! Output, with error at end: - mkbrainmask Done - Thu Jul 7 17:15:21 EDT 2011 mkbrainmask-sess done Started at Thu Jul 7 16:54:00 EDT 2011 Ended at Thu Jul 7 17:15:21 EDT 2011 preproc-sess done mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.76, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.76, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.76, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.76, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.76, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.76, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.76, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... mri_convert f.nii fskip8.nii --nskip 8 nskip = 8 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.76, -0.00683426, -0.00130865) j_ras = (0.0069578, -0.984569, -0.174858) k_ras = (-9.34106e-05, -0.174863, 0.984593) Skipping 8 frames writing to fskip8.nii... bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./009/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./009/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./009/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./011/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./011/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./011/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./013/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./013/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./013/lightboxes/tmean_lightbox.png': No such file or directory bash: /space/ventzl/36/users/RespMon12C/scripts/RM12C_lightbox.bash: No such file or directory cp: cannot stat `./015/lightboxes/tsnr_lightbox.png': No such file or directory cp: cannot stat `./015/lightboxes/tstd_lightbox.png': No such file or directory cp: cannot stat `./015/lightboxes/tmean_lightbox.png': No such file or directory bash:
Re: [Freesurfer] more on fieldsign problems-
are you sure it's registered well to the anatomical/surface? On Thu, 7 Jul 2011, Michelle Umali wrote: Hi Doug, The eccen and polar maps look ok, although activation tends to be limited to the occipital poles and lateral surface not really along the calcarine. Is it possible to find out how the colors in the eccen and polar images correspond to positions in the stimulus using rtview? There's no legend. Thanks. Michelle Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: Hi Michelle, do the eccen and polar maps look ok? Also, I would probably smooth them a little bit. The field sign calculation is basically a spatial derivative so it can be sensitive to noise. doug Michelle Umali wrote: Dear all, I've been having issues with my fieldsign images all I get are speckles. I did the following and did not get any errors: 1) ran recon-all -all 2) cut and saved occipital patches (rh.occip.patch.3d) from inflated surface 3) ran mris_flatten -w 0 distances 20 7 rh.occip.patch.3d rh.occip.patch.flat 4)mkanalysis-sess -rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 paradigm rtopy.par -nskip 4 fwhm 0 5) selxavg3-sess -a rtopy.self.rh -s sj09 6) fieldsign-sess -a rtopy.self.rh -occip -s sj09 When I looked at the fieldsign map using: 7) tksurfer-sess -a rtopy.self.rh -s sj09 -fieldsign all I got were blue and red speckles. The polar and eccentricity maps seemed ok. Any help would be great. Michelle ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Creation of normalized cortical regions of interest
Hi,freesurfers: Recently,I read a paper which used freesurfer to processed their data,this is the paper's link:http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060159 In this paper,the antor said : One of the critical steps of the whole procedure was to partition the participants' cortex into ROIs located in an identical topographic position for each participant despite interindividual anatomical variation. We used Freesurfer to register a labeled mesh from an average brain onto the brain of each individual participant, where each label corresponded to one of 66 anatomical cortical regions . This output provided for every participant a standardized partition of the cortex into 66 regional areas. In a second step, each of these regional areas were subdivided on the Freesurfer average brain into a set of small and compact regions of about 1.5 cm2, resulting in 998 ROIs covering the entire cortex. This subdivision was then registered on the individual brain using the same transformation as for the 66 regional areas thus maintaining the topological constraints of mapping. Consequently, the resulting partitions of the cortex into 66 and 998 ROIs were in anatomically closely matched positions for all participants So,I wander how can we subdivided the 66 ROIs into 998 ROIs? Thanks, wang ___ Freesurfer mailing list 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.
[Freesurfer] A question about the Freesurfer version compatibility of Tracula
Hi, I am using Tracula, a new tool that comes with version 5.1.0 of FreeSurfer. However, my data set are processed with the recon-all of an earlier version of FreeSurfer: 5.0.0. I wonder whether I need to rerun recon-all on all the subjects in the data set with 5.1.0. Would running Tracula on 5.0.0 reconstructions cause any problems that render the results unusable/not trustable? Thank you! Best, Shanqing Cai ___ Freesurfer mailing list 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.
