Re: [Freesurfer] LGI - Statistical Analysis
Hi Kenza, (I added the freesurfer mailing list in copy, please post there) You have to set the min threshold at 1 when you overlay the lGI, then you should not see any gray regions anymore. Not sure I understood your problem with the statistical analyses, maybe there is simply no significant difference? If you could complete the lGI without problem (which is the case if you have the ?h.pial_lgi files), and if you are certain of your statistical design, then it simply means that there is nothing which is more significant than the given significance threshold (you can play with the significance threshold to explore that as well, and visualize the data in plots at some vertices in qdec). Best, Marie On Apr 3, 2014, at 4:57 AM, Kenza Drissi-kaïtouni kenza.drissi-kaito...@polymtl.ca wrote: Dear Marie, I have been trying to use the lgi implemented in Freesurfer. I was able to obtain results, but unfortunately, when I overlay visualize them as an overlay of ?h.pial_lgi on the ?h.pial surface in tksurfer, I still see gray regions which shouldnt be... What can I do to fix this problem? Also, when I perform a statistical analysis on the data I obtained, only 2 small spots appear for lh and none for rh. I strongly suspect this is because of the gray regions where no lgi was apparently calculated/retained. Is it so? Thank you very much for you time, Kenza Drissi-Kaitouni B.Sc. Biomedical Engineering Ecole Polyetchnique de Montreal D.E.S.S Biomedical Engineering ___ 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] FW: registration difficulty
Hi Doug, Thanks for that, I will give that a shot and see how it looks. As for my highres hippo images, I ran the recon-all with the -hippo-subfields setting on my T1 highres whole brain anatomy file. This gave me the usual FS outputs and the extra hippo subfield volumes. I can look at these with Freeview and when I load the anatomy, the aseg and the hippo subfields, everything is fine. I then want to transform these to my diffusion space for tractography, and managed to get the anat and aseg images to align with my diffusion space B0 image but just can't get the subfields to align. I think this is due to the smaller fov of the subfields as they appear a small cubes with the hippo structures inside in the Freeview screen. Thanks again for the direction, I haven't tried the tkregister2 tool so I'll play with it and see Much appreciated. best regards Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 02 April 2014 22:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: registration difficulty should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? I did not entirely follow this thread. It sound like you have 3 volumes: orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader this will bring up the tkregister2 window and you can double check that it looks ok; save the reg. In the future you can just add --noedit and it will write the output reg without bringing up the interface. but I might not understand what is going on ... doug On 04/02/2014 03:03 PM, Erik O'Hanlon wrote: Apologies. forwarded it on now Thanks a million Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty Hi Erik can you cc the list so that others (like Doug!) can respond? thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote: Hi Bruce, Thanks so much for your reply. As for the specifics of what I have tried, so rry if it was unclear. I have performed the usual T1 based FS cortical and subcortical analysis and included the -hip_subfields so I also get all the subdivision volumes. I ha ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo lumes as masks for the purpose of tractography. I created my diff-to-orig da t file using bbregister. I then used this in the mri_vol2vol and aligned my aseg.mgz to my nodif image. This worked really well and I then used fslmaths to extract out the hippocampus from the aseg2diff. This aligns nicely. I th en tried to apply the same transformation to my subfield volumes but this di dn't work. As you suggested, and just to clarify, should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m y subfield volume to the orig.mgz and then run a second mri_vol2vol but use the nodif2orig.dat calculated before and use the nodif image as the --mov fi le and the registered subfield_2orig.nii as the --targ and use the --inv -- nearest settings as I want end up with my subfield volumes in diffusion spac e ? So sorry for the confusion, really shows my lack of experience with FS. Just getting completely mixed up at this stage. Again apologies for the lack of clarity and confusion but any pointers offer ed would be fantastic. Thanks again best regards Erik __ Hi Erik so you had a separate (presumably highres) acquisition within the hippocampus? Have you registered that with bbregister? Your best bet is probably doing so, then composing the two registrations (and inverting one, depending on what direction you want to go). cheers Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote: Dear FS experts, I am running my first FS analysis and I'm trying to register my hippocampa l subdivision volumes to my diffusion space image but cannot get good alignment. I ran my diffusion preprocessing in ExploreDTI so
Re: [Freesurfer] CWP values
Dear FreeSurfer list, When reporting coordinates of significant clusters found with Qdec, should one report 1) the Talairach coordinates displayed immediately after running the MonteCarlo correction (which I imagine are the center of gravity (CoG) coordinates?!) or 2) the max vertex Talairach coordinates displayed after using the Find clusters and go to max button? The two sets of coordinates are close for a given cluster, but never quite the same, and I don;t know which one to report. Thank you! --Francesco On 31 March 2014 20:20, Francesco Puccettone francesco.puccett...@gmail.com wrote: I see, makes sense! I had a second question, which I repeat below. When reporting significant clusters, should one refer to the cluster by 1) its annotation label, e.g. sig differences were found in the precentral gyrus, 2) its max vertex as displayed after using the Find clusters and go to max button, e.g. significant differences were found in a cluster whose maximum vertex was at (10,20,30) , or 3) by its center of gravity coordinates as displayed (I think!) immediately after running the MonteCarlo correction, e.g. significant differences were found in a cluster whose CoG was at (11,21,31)? On 31 March 2014 17:43, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: This is just the way that the interface was programmed. It was fairly easy to add a button to run the correction, more difficult to pull that information back into the interface in a reasonable way. I agree that it makes using the interface less intuitive: once you get a button to press, you come to expect that everything else will be done for you. Unfortunately, we don't have the resources to be able to do that. You'll have to look at the text file generated by QDEC doug On 03/31/2014 09:05 AM, Francesco Puccettone wrote: Hello, I see that after having qdec apply MonteCarlo correction to a certain contrast, the CWP cluster-wise probability is displayed. Those values, however, are not displayed when the Find clusters and go to max button is used, either before or after correction. WHy is that, when it seems that the CWP statistic makes sense for all 3 stages (max-vertex pre-correction, mean-cluster post-correction, max-vertex post-correction)? Thank you! --Francesco ___ 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: 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@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] preprocessing question
Hi Doug, I changed the file permissions to be executable and it passed this stage. It then gets stuck when looking for bet.fsl: # -- Using FSL's BET to Extract Brain-- # /applications/freesurfer/BSMT_project/bsmt103/bold bet.fsl /tmp/mkbrainmask_76128/in.nii /tmp/mkbrainmask_76128/brain -m -f 0.1 bet.fsl: Command not found. ERROR: bet failed Was there something wrong in the insatallation that it is missing those files? Thanks! Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question a couple of thiings to check: make sure it is exectuable and make sure that you rehash your path. Make sure that if you type fslmaths.fsl that it runs something On 04/02/2014 03:23 AM, Eiran Harel wrote: Thanks Doug, i downloaded it and now the file exists: $FREESURFER_HOME/bin/fslmaths.fsl Unfortuantely it is still not running and gives the same error when running preproc-sess: mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 ERROR: cannot find either fslmaths for avwmaths How can i proceed? Thanks, Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 12:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question thanks, it must be something in our distribution script affecting mac On 04/01/2014 05:13 PM, Markus Gschwind wrote: Thanks Doug, I notice that on my Mac build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ...I don't have fslmaths.fsl neither. There are only $ which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel /Applications/freesurfer/bin/fsl_rigid_register /Applications/freesurfer/bin/fsl_sub_mgh /Applications/freesurfer/bin/fslregister $ which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl /Applications/freesurfer/bin/fscalc.fsl /Applications/freesurfer/bin/mri_motion_correct.fsl (I never executed the above mentioned process of Eiran thoug...) Best, Markus 2014-04-01 18:36 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: That is weird. You can get a copy from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac copy it to $FREESURFER_HOME/bin/fslmaths.fsl On 04/01/2014 12:25 PM, Eiran Harel wrote: Hi Doug, No, it does not exist. What should i do? Thanks, Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question does $FREESURFER_HOME/bin/fslmaths.fsl exist? On 04/01/2014 03:59 AM, Eiran Harel wrote: Dear freesurfers, I have installed freesurfer and fsl on my Mac: * * * freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 * *Setting up environment for FreeSurfer/FS-FAST (and FSL)* *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 am trying to run Preproc-sess command: *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm 5 -fsd bold -stc odd -per-run -force* and get this error: *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0* *ERROR: cannot find either fslmaths for avwmaths* * * Any suggestions? Thanks! Eiran http://www.tasmc.org.il/be-well/Pages/default.aspx https://www.facebook.com/ichilov.medical http://twitter.com/tasmc1 http://www.youtube.com/tasmc1 http://www.tasmc.org.il/sites/en/Pages/default.aspx ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] mri_vol2surf --projopt
it sounds cool! I wonder what it does? Actually, this uses mri_compute_volume_fractions and mri_compute_intensities to build partial-volume models of the tissue and then estimate them with projopt. I haven't tried this code in a few years so you are somewhat on your own. We are hoping to clean it up and release it when I find the time. cheers Bruce On Wed, 2 Apr 2014, Douglas N Greve wrote: This is something BF added Sept 1 2009: added --projopt switch to do optimal linear estimation of gray matter values given a set of precomputed gray matter densities. I don't know what it would mean beyond that doug On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe ___ 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] preprocessing question
Hi Eiran and Doug, I do not have bet.fsl neither (c.f. previous mail with the list of what I had). It seems that there is quite some more missing in the mac build... This is what I find on my ubuntu installation freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 $ ls $FREESURFER_HOME/bin/*.fsl /usr/local/freesurfer/bin/bet.fsl /usr/local/freesurfer/bin/epidewarp.fsl /usr/local/freesurfer/bin/flirt.fsl /usr/local/freesurfer/bin/fscalc.fsl /usr/local/freesurfer/bin/fslmaths.fsl /usr/local/freesurfer/bin/fslorient.fsl /usr/local/freesurfer/bin/fslswapdim.fsl /usr/local/freesurfer/bin/mri_motion_correct.fsl /usr/local/freesurfer/bin/slicetimer.fsl $ ls $FREESURFER_HOME/bin/fsl* /usr/local/freesurfer/bin/fsl_label2voxel /usr/local/freesurfer/bin/fslmaths.fsl /usr/local/freesurfer/bin/fslorient.fsl /usr/local/freesurfer/bin/fslregister /usr/local/freesurfer/bin/fsl_rigid_register /usr/local/freesurfer/bin/fsl_sub_mgh /usr/local/freesurfer/bin/fslswapdim.fsl And this is what I have on my Mac OSX installation (freesurfer-Darwin- snowleopard-i686-stable-pub-v5.3.0) $ which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel /Applications/freesurfer/bin/fsl_rigid_register /Applications/freesurfer/bin/fsl_sub_mgh /Applications/freesurfer/bin/fslregister $ which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl /Applications/freesurfer/bin/fscalc.fsl /Applications/freesurfer/bin/mri_motion_correct.fsl Best, Markus 2014-04-03 13:35 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il: Hi Doug, I changed the file permissions to be executable and it passed this stage. It then gets stuck when looking for bet.fsl: # -- Using FSL's BET to Extract Brain-- # /applications/freesurfer/BSMT_project/bsmt103/bold bet.fsl /tmp/mkbrainmask_76128/in.nii /tmp/mkbrainmask_76128/brain -m -f 0.1 bet.fsl: Command not found. ERROR: bet failed Was there something wrong in the insatallation that it is missing those files? Thanks! Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question a couple of thiings to check: make sure it is exectuable and make sure that you rehash your path. Make sure that if you type fslmaths.fsl that it runs something On 04/02/2014 03:23 AM, Eiran Harel wrote: Thanks Doug, i downloaded it and now the file exists: $FREESURFER_HOME/bin/fslmaths.fsl Unfortuantely it is still not running and gives the same error when running preproc-sess: mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 ERROR: cannot find either fslmaths for avwmaths How can i proceed? Thanks, Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [ gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 12:41 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question thanks, it must be something in our distribution script affecting mac On 04/01/2014 05:13 PM, Markus Gschwind wrote: Thanks Doug, I notice that on my Mac build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ...I don't have fslmaths.fsl neither. There are only $ which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel /Applications/freesurfer/bin/fsl_rigid_register /Applications/freesurfer/bin/fsl_sub_mgh /Applications/freesurfer/bin/fslregister $ which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl /Applications/freesurfer/bin/fscalc.fsl /Applications/freesurfer/bin/mri_motion_correct.fsl (I never executed the above mentioned process of Eiran thoug...) Best, Markus 2014-04-01 18:36 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: That is weird. You can get a copy from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac copy it to $FREESURFER_HOME/bin/fslmaths.fsl On 04/01/2014 12:25 PM, Eiran Harel wrote: Hi Doug, No, it does not exist. What should i do? Thanks, Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu mailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu] Sent: Tuesday, April 01, 2014 7:16 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
[Freesurfer] reading colorized labels in tcl file to tksurfer...
Hi all -- I have a process that generates a list of ROIs (from aparc.annot) based on some cost condition. I wanted to view these labeled ROIs in 'tksurfer'. I created the following rough tcl script: 'label_load.tcl' set label lh.bankssts.label ; read_and_color_labeled_vertices 255 255 0 set label lh.caudalanteriorcingulate.label ; read_and_color_labeled_vertices 255 255 10 set label lh.caudalmiddlefrontal.label ; read_and_color_labeled_vertices 255 255 20 set label lh.cuneus.label ; read_and_color_labeled_vertices 255 255 30 set label lh.inferiorparietal.label ; read_and_color_labeled_vertices 255 255 40 set label lh.lateraloccipital.label ; read_and_color_labeled_vertices 255 255 50 and then ran with tksurfer subj hemi surface -tcl label_load.tcl The labels all load, but they are all the same teal-like color. I'm guessing that I am using the wrong tksurfer internal command... I have looked through the wiki, but didn't immediately see a solution. Help? Best -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ 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] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist
Hi All, mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for ex. --projfrac 0.5 for a given subject? (actually similar to what was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A, http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf). Thank you very much in advance for your help! All the best, Ruthger ___ 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] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist
Hi Ruthger! Use mris_expand to create a surf inside or outside of white e.g. mris_expand surf/lh.white -1 surf/lh.white_1mm_inside # use positive values for outside ?h.white border mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness # this samples in % of GM thickness, use positive values for outside white Cheers! Markus 2014-04-03 16:24 GMT+02:00 Righart, Ruthger righ...@lrz.tu-muenchen.de: Hi All, mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for ex. --projfrac 0.5 for a given subject? (actually similar to what was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A, http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf). Thank you very much in advance for your help! All the best, Ruthger ___ 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] FW: registration difficulty
Hi Doug, I managed to get the subfield volumes aligned at last. I used bbregister to get the dat file for the No_diff2orig transform. Then used tkregister2 to get the dat for my subfield volume to orig. Used mdi_vol2vol to align my subfield vol to the orig.mgz. Finally aligned the subfieldaligned_orig file to the No_diff image using mdi_vol2vol with the regsiterNodiff2orig.dat file and the --inv flag. I know it's probably not the best way to do it but it all aligns nicely. Thanks for the pointers Cheers Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 03 April 2014 10:23 To: Freesurfer support list Subject: Re: [Freesurfer] FW: registration difficulty Hi Doug, Thanks for that, I will give that a shot and see how it looks. As for my highres hippo images, I ran the recon-all with the -hippo-subfields setting on my T1 highres whole brain anatomy file. This gave me the usual FS outputs and the extra hippo subfield volumes. I can look at these with Freeview and when I load the anatomy, the aseg and the hippo subfields, everything is fine. I then want to transform these to my diffusion space for tractography, and managed to get the anat and aseg images to align with my diffusion space B0 image but just can't get the subfields to align. I think this is due to the smaller fov of the subfields as they appear a small cubes with the hippo structures inside in the Freeview screen. Thanks again for the direction, I haven't tried the tkregister2 tool so I'll play with it and see Much appreciated. best regards Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: 02 April 2014 22:35 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: registration difficulty should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? I did not entirely follow this thread. It sound like you have 3 volumes: orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader this will bring up the tkregister2 window and you can double check that it looks ok; save the reg. In the future you can just add --noedit and it will write the output reg without bringing up the interface. but I might not understand what is going on ... doug On 04/02/2014 03:03 PM, Erik O'Hanlon wrote: Apologies. forwarded it on now Thanks a million Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 02 April 2014 19:58 To: Erik O'Hanlon Subject: Re: [Freesurfer] FW: registration difficulty Hi Erik can you cc the list so that others (like Doug!) can respond? thanks Bruce On Wed, 2 Apr 2014, Erik O'Hanlon wrote: Hi Bruce, Thanks so much for your reply. As for the specifics of what I have tried, so rry if it was unclear. I have performed the usual T1 based FS cortical and subcortical analysis and included the -hip_subfields so I also get all the subdivision volumes. I ha ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo lumes as masks for the purpose of tractography. I created my diff-to-orig da t file using bbregister. I then used this in the mri_vol2vol and aligned my aseg.mgz to my nodif image. This worked really well and I then used fslmaths to extract out the hippocampus from the aseg2diff. This aligns nicely. I th en tried to apply the same transformation to my subfield volumes but this di dn't work. As you suggested, and just to clarify, should I now rerun the bbregsiter and create a new dat file for the subfield volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m y subfield volume to the orig.mgz and then run a second mri_vol2vol but use the nodif2orig.dat calculated before and use the nodif
Re: [Freesurfer] preprocessing question
Hi, I seem to have even less files: Eran-Harels-MacBook-Pro:/applications/freesurfer] eiran% which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl [Eran-Harels-MacBook-Pro:/applications/freesurfer] eiran% which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel Eiran From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [markus.gschw...@gmail.com] Sent: Thursday, April 03, 2014 3:43 PM To: Freesurfer support list Subject: Re: [Freesurfer] preprocessing question Hi Eiran and Doug, I do not have bet.fsl neither (c.f. previous mail with the list of what I had). It seems that there is quite some more missing in the mac build... This is what I find on my ubuntu installation freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 $ ls $FREESURFER_HOME/bin/*.fsl /usr/local/freesurfer/bin/bet.fsl /usr/local/freesurfer/bin/epidewarp.fsl /usr/local/freesurfer/bin/flirt.fsl /usr/local/freesurfer/bin/fscalc.fsl /usr/local/freesurfer/bin/fslmaths.fsl /usr/local/freesurfer/bin/fslorient.fsl /usr/local/freesurfer/bin/fslswapdim.fsl /usr/local/freesurfer/bin/mri_motion_correct.fsl /usr/local/freesurfer/bin/slicetimer.fsl $ ls $FREESURFER_HOME/bin/fsl* /usr/local/freesurfer/bin/fsl_label2voxel /usr/local/freesurfer/bin/fslmaths.fsl /usr/local/freesurfer/bin/fslorient.fsl /usr/local/freesurfer/bin/fslregister /usr/local/freesurfer/bin/fsl_rigid_register /usr/local/freesurfer/bin/fsl_sub_mgh /usr/local/freesurfer/bin/fslswapdim.fsl And this is what I have on my Mac OSX installation (freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0) $ which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel /Applications/freesurfer/bin/fsl_rigid_register /Applications/freesurfer/bin/fsl_sub_mgh /Applications/freesurfer/bin/fslregister $ which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl /Applications/freesurfer/bin/fscalc.fsl /Applications/freesurfer/bin/mri_motion_correct.fsl Best, Markus 2014-04-03 13:35 GMT+02:00 Eiran Harel eir...@tlvmc.gov.ilmailto:eir...@tlvmc.gov.il: Hi Doug, I changed the file permissions to be executable and it passed this stage. It then gets stuck when looking for bet.fsl: # -- Using FSL's BET to Extract Brain-- # /applications/freesurfer/BSMT_project/bsmt103/bold bet.fsl /tmp/mkbrainmask_76128/in.nii /tmp/mkbrainmask_76128/brain -m -f 0.1 bet.fsl: Command not found. ERROR: bet failed Was there something wrong in the insatallation that it is missing those files? Thanks! Eiran From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 5:21 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question a couple of thiings to check: make sure it is exectuable and make sure that you rehash your path. Make sure that if you type fslmaths.fsl that it runs something On 04/02/2014 03:23 AM, Eiran Harel wrote: Thanks Doug, i downloaded it and now the file exists: $FREESURFER_HOME/bin/fslmaths.fsl Unfortuantely it is still not running and gives the same error when running preproc-sess: mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 ERROR: cannot find either fslmaths for avwmaths How can i proceed? Thanks, Eiran From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu] Sent: Wednesday, April 02, 2014 12:41 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] preprocessing question thanks, it must be something in our distribution script affecting mac On 04/01/2014 05:13 PM, Markus Gschwind wrote: Thanks Doug, I notice that on my Mac build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 ...I don't have fslmaths.fsl neither. There are only $ which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_label2voxel /Applications/freesurfer/bin/fsl_rigid_register /Applications/freesurfer/bin/fsl_sub_mgh /Applications/freesurfer/bin/fslregister $ which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl /Applications/freesurfer/bin/fscalc.fsl /Applications/freesurfer/bin/mri_motion_correct.fsl (I never executed the above mentioned process of Eiran thoug...) Best, Markus 2014-04-01 18:36 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] missing Freesurfer wiki pages
Hi Gabor, Thanks, should be fixed now. Any of the links with the _tktools suffix can be replaced with _freeview to view an alternate version of the wiki page using freeview commands. -Louis On Tue, 1 Apr 2014, Gabor Perlaki wrote: Dear all, Most of the links on https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction page do not work. If I clik for example on FsTutorial/SkullStripFix the following message will popup: This page does not exist yet. You can create a new empty page, or use one of the page templates. Is there a new page for the recommended workflow which works fine? Thanks, Gabor ___ 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] Standard surface tessellation
Dear FreeSurfer, I am a beginner in FreeSurfer and wonder if it is possible in FreeSurfer to apply the same triangulation across multiple subjects, i.e. the same number of vertices and triangles at the anatomically identical locations. For instance, I have 10 subjects and want to have pial (or white matter) surfaces of individual subjects consisting of 14000 vertices which are anatomically matched. Any suggestion will be greatly appreciated. Justin. ___ 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] Converting a volume from MNI152 to subject space
Hi Freesurfers, I am trying to convert a volume from MNI152 to subject space. I tried to do what this previous question suggested: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-December/034722.html I tried to create a registration matrix from subject space to MNI152: mni152reg --s AL15 However, this error appeared: ... mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345': Permission denied ... writing to /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345/refvol.fslregister.nii... ERROR: failure writing /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.28345/refvol.fslregister.nii I would then have used this command: mri_label2vol --seg lh.AItou.nii.gz --reg AL15/mri/transforms/reg.mni152.2mm.dat --invertmtx --o lh.aitou.AL15.nii.gz --temp AL15/mri/orig.mgz How can I make the mni152reg command work? Is this the correct way to do this? Thanks! Best, Omar ___ 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] Displaying parcellated ROI in color but remainder of brain in grey
Hi Again Doug, I was able to get what I was looking for after I modified my ctab file slightly and used tksurfer instead of freeview to display the images. I am hoping, however, that it is still possible to get things to work in freeview. For the ctab file, I put my 6 parcellated ROI's at the start of the ctab file and numbered them 1 to 6. I numbered the remaining regions 7-75. In freeview the ROI's were in color but the remainder of the brain was black (not what I wanted). However in tksurfer, everything looked good (brain in grey and ROI's in different colors). Do you think it would be possible to display these images properly in freeview as well? Thank you very much for your time, Laura On Wed, Apr 2, 2014 at 10:05 AM, Laura Taylor taylor.cnos@gmail.comwrote: Hi Doug, Thank you for your reply. This was my mris_label2annot command line: woodward@Bambi:~$ mris_label2annot --s TGT_N61AvgSubject --h rh --ctab /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab --a Comp2RH_TGTN61_properGreyRH --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label --l /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label This is the terminal output: Reading ctab /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab Number of ctab entries 76 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /home/woodward cmdline mris_label2annot --s TGT_N61AvgSubject --h rh --ctab /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab --a Comp2RH_TGTN61_properGreyRH --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label --l /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label sysname Linux hostname Bambi machine x86_64 user woodward subject TGT_N61AvgSubject hemirh SUBJECTS_DIR /Data/freesurfer/subjects ColorTable /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab AnnotName Comp2RH_TGTN61_properGreyRH nlables 6 LabelThresh 0 0.00 Loading /Data/freesurfer/subjects/TGT_N61AvgSubject/surf/rh.orig 1 8355711 G_and_S_frontomargin 2 8355711 G_and_S_occipital_inf 3 8355711 G_and_S_paracentral 4 8355711 G_and_S_subcentral 5 8355711 G_and_S_transv_frontopol 6 8355711 G_and_S_cingul-Ant Mapping unhit to unknown Found 154540 unhit vertices Writing annot to /Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_properGreyRH.annot colortab file: /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab 0 Unknown 0 0 00 1 G_and_S_frontomargin 127 127 127 0 2 G_and_S_occipital_inf127 127 127 0 3 G_and_S_paracentral 127 127 127 0 4 G_and_S_subcentral 127 127 127 0 5 G_and_S_transv_frontopol 127 127 127 0 6 G_and_S_cingul-Ant 127 127 127 0 7 G_and_S_cingul-Mid-Ant 127 127 127 0 8 G_and_S_cingul-Mid-Post 127 127 127 0 9 G_cingul-Post-dorsal 127 127 127 0 10 G_cingul-Post-ventral127 127 127 0 11 G_cuneus 127 127 127 0 12 G_front_inf-Opercular127 127 127 0 13 G_front_inf-Orbital 127 127 127 0 14 G_front_inf-Triangul 127 127 127 0 15 G_front_middle 127 127 127 0 16 G_front_sup 127 127 127 0 17 G_Ins_lg_and_S_cent_ins 127 127 127 0 18 G_insular_short 127 127 127 0 19 G_occipital_middle 127 127 127 0 20 G_occipital_sup 127 127 127 0 21 G_oc-temp_lat-fusifor60 20 1400 22 G_oc-temp_med-Lingual 220 180 1400 23 G_oc-temp_med-Parahip127 127 127 0 24 G_orbital127 127 127 0 25 G_pariet_inf-Angular 127 127 127 0 26 G_pariet_inf-Supramar
Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey
Hi Laura, I am facing the same problem when using freeview. Can you tell me what was your commandline that solved the problem in tksurfer? How did you get the ctab file and did you edit it using the RGB color codes? Thanks in advance. Shantanu On Thu, April 3, 2014 6:55 pm, Laura Taylor wrote: Hi Again Doug, I was able to get what I was looking for after I modified my ctab file slightly and used tksurfer instead of freeview to display the images. I am hoping, however, that it is still possible to get things to work in freeview. For the ctab file, I put my 6 parcellated ROI's at the start of the ctab file and numbered them 1 to 6. I numbered the remaining regions 7-75. In freeview the ROI's were in color but the remainder of the brain was black (not what I wanted). However in tksurfer, everything looked good (brain in grey and ROI's in different colors). Do you think it would be possible to display these images properly in freeview as well? Thank you very much for your time, Laura On Wed, Apr 2, 2014 at 10:05 AM, Laura Taylor taylor.cnos@gmail.comwrote: Hi Doug, Thank you for your reply. This was my mris_label2annot command line: woodward@Bambi:~$ mris_label2annot --s TGT_N61AvgSubject --h rh --ctab /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab --a Comp2RH_TGTN61_properGreyRH --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label --l /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label This is the terminal output: Reading ctab /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab Number of ctab entries 76 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /home/woodward cmdline mris_label2annot --s TGT_N61AvgSubject --h rh --ctab /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab --a Comp2RH_TGTN61_properGreyRH --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label --l /Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label --l /Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label sysname Linux hostname Bambi machine x86_64 user woodward subject TGT_N61AvgSubject hemirh SUBJECTS_DIR /Data/freesurfer/subjects ColorTable /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab AnnotName Comp2RH_TGTN61_properGreyRH nlables 6 LabelThresh 0 0.00 Loading /Data/freesurfer/subjects/TGT_N61AvgSubject/surf/rh.orig 1 8355711 G_and_S_frontomargin 2 8355711 G_and_S_occipital_inf 3 8355711 G_and_S_paracentral 4 8355711 G_and_S_subcentral 5 8355711 G_and_S_transv_frontopol 6 8355711 G_and_S_cingul-Ant Mapping unhit to unknown Found 154540 unhit vertices Writing annot to /Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_properGreyRH.annot colortab file: /Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab 0 Unknown 0 0 00 1 G_and_S_frontomargin 127 127 127 0 2 G_and_S_occipital_inf127 127 127 0 3 G_and_S_paracentral 127 127 127 0 4 G_and_S_subcentral 127 127 127 0 5 G_and_S_transv_frontopol 127 127 127 0 6 G_and_S_cingul-Ant 127 127 127 0 7 G_and_S_cingul-Mid-Ant 127 127 127 0 8 G_and_S_cingul-Mid-Post 127 127 127 0 9 G_cingul-Post-dorsal 127 127 127 0 10 G_cingul-Post-ventral127 127 127 0 11 G_cuneus 127 127 127 0 12 G_front_inf-Opercular127 127 127 0 13 G_front_inf-Orbital 127 127 127 0 14 G_front_inf-Triangul 127 127 127 0 15 G_front_middle 127 127 127 0 16 G_front_sup 127 127 127 0 17 G_Ins_lg_and_S_cent_ins 127 127 127 0 18 G_insular_short 127 127 127 0 19 G_occipital_middle 127 127 127 0 20 G_occipital_sup 127 127 127 0 21 G_oc-temp_lat-fusifor
Re: [Freesurfer] Subcortical segmentation for PAG
no, not yet. Sorry. We have been talking about it Bruce On Thu, 3 Apr 2014, Jeni Chen wrote: Hi, Just wondering if the periaqueductal gray is part of the automatic segmentation process and if we can obtain the volume. I checked the aseg table but didn't see it, however, I somehow remember seeing it before... Was it ever included? Thanks. Jeni ___ 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] TRACULA longitudinal stream - length of Center variable
Dear TRACULA experts, I have used the longitudinal version and find that for some subjects' tracts Len_Min is larger than Len_Center. How is this possible? (An extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.) Best, Vincent --- This email is free from viruses and malware because avast! Antivirus protection is active. http://www.avast.com ___ 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.
