Hi Bruce, I was running multiple recon-all scripts at the same time. Let me try a fresh run on that subject to see if that's the issue. If I get another error, I will write back.
******************************************** Michael Amlung, Ph.D. Assistant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter Boris Centre for Addictions Research 100 West 5th Street Hamilton, Ontario L8N 3K7 Canada Telephone: (+1) 905-522-1155, ext. 39014 Email: amlu...@mcmaster.ca Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of freesurfer-requ...@nmr.mgh.harvard.edu Sent: Wednesday, September 09, 2015 12:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 139, Issue 14 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Creating label from Tal coordinates (Rodriguez-Thompson, Anais) 2. Re: Creating label from Tal coordinates (Douglas N Greve) 3. Re: mri_glmfit-sim error (Douglas N Greve) 4. Re: conjunction map (Douglas N Greve) 5. Re: mri_glmfit-sim error (Xiaomin Yue) 6. Functional connectivity with volume label (Rodriguez-Thompson, Anais) 7. Automaticky: Jan Sanda is out of the office (a vr?t? se ne 13.9.2015) (jan.sa...@fnmotol.cz) 8. Re: mri_compute_volume_fractions not filling some sulci properly (Bruce Fischl) 9. Help with recon-all (Amlung, Michael) 10. Re: mri_compute_volume_fractions not filling some sulci properly (Bruce Fischl) 11. Re: Help with recon-all (Bruce Fischl) 12. TrackVis Transforms (Thomas Potrusil) 13. Re: TrackVis Transforms (Anastasia Yendiki) 14. Freesurfer/Qdec brain images (Lim, Lena) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Sep 2015 20:27:10 +0000 From: "Rodriguez-Thompson, Anais" <arodriguez-thomp...@mgh.harvard.edu> Subject: Re: [Freesurfer] Creating label from Tal coordinates To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <2d9198b56d6d9a41942f94ef7248a74f05229...@phsx10mb19.partners.org> Content-Type: text/plain; charset="us-ascii" Hi Doug, I didn't see a colored dot. Unlike tksurfer, I didn't see a fill option to create a label from a point. Is there something I should do other than moving the cursor to my point of interest and then "save label as?" Thanks, Anais ________________________________________ 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: Tuesday, September 08, 2015 2:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Creating label from Tal coordinates There are no points in the label. I'm not sure that you actually created a label. Did you have tkmedit configured to draw labels? Actually, I think it open that way... Did you see a colored dot where your label was? On 09/08/2015 02:04 PM, Rodriguez-Thompson, Anais wrote: > Hi Freesurfer experts, > > I am trying to create a label from Talairach coordinates. I loaded the > fsaverage brain in tkmedit (tkmedit fsaverage orig.mgz) and entered the > coordinates 0 -16 -6 (our coordinates of interest). From here I saved the > label using "save label as". However, when I try to load this label, I get > the error "tkmedit couldn't read the label you specified. This could be > because the format wasn't valid or the file wasn't found." > > The actual label file reads: > #!ascii label > /cluster/roffman/users/Stable5_PerRun/fsaverage1/label/vta , from > subject fsaverage vox2ras=TkReg > 0 > > Do you know why I'm having trouble making/visualizing a label created from > Tal coordinates and how I can do so? > > Thanks, > Anais > _______________________________________________ > 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 ------------------------------ Message: 2 Date: Tue, 08 Sep 2015 16:59:35 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Creating label from Tal coordinates To: freesurfer@nmr.mgh.harvard.edu Message-ID: <55ef4c37.1050...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed use the middle mouse button to create the label, then save it On 09/08/2015 04:27 PM, Rodriguez-Thompson, Anais wrote: > Hi Doug, > > I didn't see a colored dot. Unlike tksurfer, I didn't see a fill option to > create a label from a point. Is there something I should do other than moving > the cursor to my point of interest and then "save label as?" > > Thanks, > Anais > ________________________________________ > 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: Tuesday, September 08, 2015 2:47 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Creating label from Tal coordinates > > There are no points in the label. I'm not sure that you actually > created a label. Did you have tkmedit configured to draw labels? > Actually, I think it open that way... Did you see a colored dot where your > label was? > > On 09/08/2015 02:04 PM, Rodriguez-Thompson, Anais wrote: >> Hi Freesurfer experts, >> >> I am trying to create a label from Talairach coordinates. I loaded the >> fsaverage brain in tkmedit (tkmedit fsaverage orig.mgz) and entered the >> coordinates 0 -16 -6 (our coordinates of interest). From here I saved the >> label using "save label as". However, when I try to load this label, I get >> the error "tkmedit couldn't read the label you specified. This could be >> because the format wasn't valid or the file wasn't found." >> >> The actual label file reads: >> #!ascii label >> /cluster/roffman/users/Stable5_PerRun/fsaverage1/label/vta , from >> subject fsaverage vox2ras=TkReg >> 0 >> >> Do you know why I'm having trouble making/visualizing a label created from >> Tal coordinates and how I can do so? >> >> Thanks, >> Anais >> _______________________________________________ >> 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 > > _______________________________________________ > 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/ ------------------------------ Message: 3 Date: Tue, 08 Sep 2015 17:03:23 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit-sim error To: freesurfer@nmr.mgh.harvard.edu Message-ID: <55ef4d1b.7040...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Use "abs" not "<abs>" On 09/04/2015 03:20 PM, Xiaomin Yue wrote: > Hi, > > I got this error when run mri_glmfit-sim: missing name for redirect. > I am running freesurfer 5.3. the command is: mri_glmfit --glmdir > ces.nii --cache 2 --sim-sign <abs>. The ces.nii was generated from > group level analysis (isxconcat-sess). > > Thanks for your help. > > Xiaomin > > > _______________________________________________ > 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/ ------------------------------ Message: 4 Date: Tue, 08 Sep 2015 17:03:58 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] conjunction map To: freesurfer@nmr.mgh.harvard.edu Message-ID: <55ef4d3e.3090...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed no, use mri_concat with the --conjunct option On 09/04/2015 12:08 PM, std...@virgilio.it wrote: > Hi list, > > is possible to obtained a conjunction map from vlrmerge command on > FS-FAST (resting state) results? > > > Stefano > > > _______________________________________________ > 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/ ------------------------------ Message: 5 Date: Tue, 8 Sep 2015 21:34:34 +0000 From: Xiaomin Yue <yu...@hotmail.com> Subject: Re: [Freesurfer] mri_glmfit-sim error To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <blu406-eas14916d41207a9074635a75bb3...@phx.gbl> Content-Type: text/plain; charset="utf-8" Thanks Xiaomin On Tue, Sep 8, 2015 at 2:03 PM -0700, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: Use "abs" not "<abs>" On 09/04/2015 03:20 PM, Xiaomin Yue wrote: > Hi, > > I got this error when run mri_glmfit-sim: missing name for redirect. > I am running freesurfer 5.3. the command is: mri_glmfit --glmdir > ces.nii --cache 2 --sim-sign <abs>. The ces.nii was generated from > group level analysis (isxconcat-sess). > > Thanks for your help. > > Xiaomin > > > _______________________________________________ > 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150908/b4a9ac4a/attachment.html ------------------------------ Message: 6 Date: Tue, 8 Sep 2015 22:42:09 +0000 From: "Rodriguez-Thompson, Anais" <arodriguez-thomp...@mgh.harvard.edu> Subject: [Freesurfer] Functional connectivity with volume label To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <2d9198b56d6d9a41942f94ef7248a74f05229...@phsx10mb19.partners.org> Content-Type: text/plain; charset="us-ascii" Hi Freesurfer experts, I'm trying to run a functional connectivity analysis using a label that was created in the volume (vta.label). I have a few questions about how I would do this (compared to a label created on surface). Usually, we create a smoothed mask using the commands mri_label2label --s fsaverage --regmethod surface --hemi {hemi} --srclabel $SUBJECTS_DIR/fsaverage1/label/{label}.label --trglabel $SUBJECTS_DIR/fsaverage1/label/junk.label --outmask /cluster/roffman/users/Stable5_PerRun/fsaverage1/mri/{label}_sm00_bin.mgh mris_fwhm --i /cluster/roffman/users/Stable5_PerRun/fsaverage1/mri/{label}_sm00_bin.mgh --fwhm 4 --smooth-only --o /cluster/roffman/users/Stable5_PerRun/fsaverage1/mri/{label}_sm04.mgh --s fsaverage --hemi rh end I tried running mri_label2label using --regmethod volume, but the command window says "ERROR: cannot specify outmask with vol reg method" Do you know how I can create a smoothed mask from a volume label? And then once I create the mask, in order to apply the mask from fsaverage to each individual subject, would I use mri_vol2vol? Thanks, Anais ------------------------------ Message: 7 Date: Wed, 9 Sep 2015 09:29:42 +0200 From: jan.sa...@fnmotol.cz Subject: [Freesurfer] Automaticky: Jan Sanda is out of the office (a vr?t? se ne 13.9.2015) To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <of5d8cde08.af77cb0d-onc1257ebb.00292c1d-c1257ebb.00292...@fnmotol.cz> Content-Type: text/plain; charset=windows-1250 Od st 9.9.2015 do ne 13.9.2015 jsem mimo kancel??. Pozn?mka: Toto je automatick? odpov?? na va?i zpr?vu "[Freesurfer] Functional connectivity with volume label" odeslanou dne 9.9.2015 0:42:09. Toto je jedin? ozn?men?, kter? obdr??te v dob? nep??tomnosti t?to osoby. ------------------------------ Message: 8 Date: Wed, 9 Sep 2015 08:35:32 -0400 (EDT) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci properly To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.lrh.2.20.1509090834380.17...@gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-7" Hi Sebastien it's pretty hard to tell what's going on from a couple of slices. What was the command line you used? If you upload the subject I'll take a look (I'll need the exact command lines you ran as well). cheers Bruce On Tue, 8 Sep 2015, Sebastien Proulx wrote: > > My images don?t seem to have come out. Here it is again in attachments > instead of inserts. > > ? > > In csf.png, we see that the calcarine was not completely filled with > CSF by mri_compute_volume_fractions. > > ? > > In gm.png, it is instead filled with gray matter. > > ? > > In ribbon.png, we see that the standard freesurfer pipeline did > correctly assigned to same spot to non-gray matter, suggesting that > the problem comes from mri_compute_volume_fractions, and not from some > failure of the surface reconstruction. > > ? > > Thanks a lot for your much needed help and > > Have a very good day! > > > ------------------------------ Message: 9 Date: Wed, 9 Sep 2015 12:42:20 +0000 From: "Amlung, Michael" <amlu...@mcmaster.ca> Subject: [Freesurfer] Help with recon-all To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <b897b38a9f69b844b9925006fefe67e56cb7b...@fhsdb2d11-1.csu.mcmaster.ca> Content-Type: text/plain; charset="us-ascii" Hi all, I am new to FreeSurfer, so this may be a novice question. We are running recon-all and the script finished without errors for all of our subjects except for one. I have opened the recon-all.log file to examine the output, but am not sure where to locate the error. The last thing printed to the terminal window was a segmentation fault. Would someone be willing to help me interpret my log file to find where the error occurred. Thanks for the assistance. Michael Amlung ******************************************** Michael Amlung, Ph.D. Assistant Professor Department of Psychiatry and Behavioural Neurosciences DeGroote School of Medicine McMaster University Peter Boris Centre for Addictions Research 100 West 5th Street Hamilton, Ontario L8N 3K7 Canada Telephone: (+1) 905-522-1155, ext. 39014 Email: amlu...@mcmaster.ca Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150909/a6f6ca3e/attachment.html ------------------------------ Message: 10 Date: Wed, 9 Sep 2015 08:44:24 -0400 (EDT) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci properly To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.lrh.2.20.1509090843110.17...@gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-7" p.s. you can try increasing the resolution of the intermediate volumes using the -r switch. The default is 0.5. Try 0.25 (although this will take 8 times the memory and time I think). Make sure to put the -r 0.25 before before the mandatory options. If this does make things look significantly better please let us know On Tue, 8 Sep 2015, Sebastien Proulx wrote: > > My images don?t seem to have come out. Here it is again in attachments > instead of inserts. > > ? > > In csf.png, we see that the calcarine was not completely filled with > CSF by mri_compute_volume_fractions. > > ? > > In gm.png, it is instead filled with gray matter. > > ? > > In ribbon.png, we see that the standard freesurfer pipeline did > correctly assigned to same spot to non-gray matter, suggesting that > the problem comes from mri_compute_volume_fractions, and not from some > failure of the surface reconstruction. > > ? > > Thanks a lot for your much needed help and > > Have a very good day! > > > ------------------------------ Message: 11 Date: Wed, 9 Sep 2015 08:46:56 -0400 (EDT) From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Help with recon-all To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.lrh.2.20.1509090845400.17...@gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="iso-8859-15" Hi Michael sure, send us the recon-all.log. We don't get many segfaults, and usually they are because you ran out of RAM or disk space. Were you running other things on the machine at the same time? We will need this info: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting cheers Bruce On Wed, 9 Sep 2015, Amlung, Michael wrote: > > Hi all, > > ? > > I am new to FreeSurfer, so this may be a novice question. We are > running recon-all and the script finished without errors for all of > our subjects except for one. I have opened the recon-all.log file to > examine the output, but am not sure where to locate the error. The > last thing printed to the terminal window was a segmentation fault. > Would someone be willing to help me interpret my log file to find > where the error occurred. Thanks for the assistance. > > ? > > Michael Amlung > > ? > > ? > > ? > > ******************************************** > > Michael Amlung, Ph.D. > > Assistant Professor > > ? > > Department of Psychiatry and Behavioural Neurosciences > > DeGroote School of Medicine > > McMaster University > > ? > > Peter Boris Centre for Addictions Research > > 100 West 5th Street > > Hamilton, Ontario L8N 3K7? > > Canada > > ? > > Telephone: (+1) 905-522-1155, ext. 39014 > > Email: amlu...@mcmaster.ca > > Web: http://fhs.mcmaster.ca/psychiatryneuroscience/AmlungMichael.html > > ? > > > ------------------------------ Message: 12 Date: Wed, 9 Sep 2015 15:40:33 +0200 From: "Thomas Potrusil" <am-dam-...@gmx.at> Subject: [Freesurfer] TrackVis Transforms To: freesurfer@nmr.mgh.harvard.edu Message-ID: <trinity-0996c35e-3597-4c23-ba98-f2c29136e602-1441806032918@3capp-gmx-bs04> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150909/0d06f5c8/attachment.html ------------------------------ Message: 13 Date: Wed, 9 Sep 2015 09:51:34 -0400 (EDT) From: Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] TrackVis Transforms To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.lrh.2.20.1509090948350.20...@door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Thomas - If you have a .mat transform, try dmri_trk2trk to apply it to a .trk file. You have to specify reference volumes for the input and output space. Best, a.y On Wed, 9 Sep 2015, Thomas Potrusil wrote: > Dear FreeSurfers !! > I?m trying to bring a trackvis .trk file to freesurfer space but fail > completely... > I tried to execute the code descibed on the following page: > https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms > and also read the detailes regarding trk-(header)-data described here: > http://www.trackvis.org/docs/?subsect=fileformat > ... but without success ! > Can you please provide me an example how to successfully use the following > code on my command line: > > trk_verts_crs.xyz = trk_verts.xyz / (trkHeader.voxel_size[0], > trkHeader.voxel_size[1], trkHeader.voxel > _size[2]) > > trk_verts_tkreg = CRS2XYZtkreg * trk_verts_crs I?m very thankful for > your help, thankx a lot, Thomas > > ------------------------------ Message: 14 Date: Wed, 9 Sep 2015 13:53:21 +0000 From: "Lim, Lena" <lena....@kcl.ac.uk> Subject: [Freesurfer] Freesurfer/Qdec brain images To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <am2pr03mb0851424cf271de7e41268c33c2...@am2pr03mb0851.eurprd03.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Dear Experts, I need some help regarding saving the brain images in Freesurfer/Qdec please: 1) Can I save the brain regions shown in Qdec group analysis as other files and view them in MRIcroN etc or does it only allow us to save the images as tiff files (inflated medial, inflated lateral, pial medial, pial lateral). How can I get more images than these 4? 2) Can I see the other coordinates within the cluster of regions besides the peak? E.g. The cluster spreads from precuneus to the parietal area so can I get the coordinates for the parietal region as well besides the peak given in the table (precuneus)? 3) Where can I get info re the BA nos of the brain regions shown in the Qdec analysis as well please? Many thanks, Lena -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150909/1f667325/attachment.html ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 139, Issue 14 ******************************************* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
