[Freesurfer] Incorporating (high resolution) T2- and FLAIR volumes
Hi FreeSurfer experts! We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be fine to use the T2 / FLAIR volumes to improve the segmentation and to perform a couple additional analyses using FS. This leads to the following questions: 1) How do I incorporate T2/Flair volumes into the recon all processing stream? a) Would it be like: recon-all bert -all -T2 /luke/xyz/007-T2.nii ? b) What is expected to get the better results regarding the pial surface: FLAIR or T2? (both are at 1x1x1mm) 2) Is there any module in FS to detect white matter lesions? 3) How can I perform myelin mapping using the ratio method (T1w/T2w)? Or do I have to switch to Caret? Many thanks in advance for your help and advice! Best wishes, Luke___ 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] Problem with tracula: incomplete or lacking tracts
Hi Analstasia, as you suggest, adjusting brain mask the tracts are better. Now I'd like to perform trac-all with new version by using a new configuration file. I do not understand what I should do for: 1- set b0mlist2- set b0plist Thanks. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 20.22 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: Problem with tracula: incomplete or lacking tracts Yes, it's a warning, not an error. On Mon, 25 Mar 2013, std...@virgilio.it wrote: Hi Anastasia,now I have correct the nodif mask and run again trac-all. Is normal WARN: Could not find satisfactory control point fit - try 83Finding center streamline during -prior? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 18.02 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts I also remember that your brain masks had some big chunks of brain missing. Was whatever caused that fixed as well? On Mon, 25 Mar 2013, std...@virgilio.it wrote: Yes, I fix them. I'm attacking the maps after the last trac-all. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 17.26 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - As I recall, we established that your bvecs were wrong. Did you fix them? a.y On Mon, 25 Mar 2013, std...@virgilio.it wrote: Hi Anastasia, I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends from an error in my configuration file? I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? Thanks, Stefano On Fri, 22 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi Anastasia - I attacked the screenshots. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 1.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - There's nothing in these screenshots that tells you that the eigenvectors are correct. These are vectors, so the way to check them is to display them as lines. You display dtifit_V1 as lines, overlaid on dtifit_FA. Then you see if the lines point in the right direction. a.y On Fri, 22 Mar 2013, std...@virgilio.it wrote: Here they are attacked. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 21-mar-2013 21.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts Can you send a screenshot that shows dtifit_V1 and dtifit_FA? On Thu, 21 Mar 2013, std...@virgilio.it wrote: I have checked the gradient directions. How can I resolve the brain mask problem. Can I send you my files of this subject? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 22.46 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check that the gradient directions are correct, so you know if you have multiple problems or just one. The FA
[Freesurfer] qdec covariates
Hi list,I'm performing qdec. This my file.dat1 diagnosis discrete 21 Pathology2 Controls2 Thickness_lh continuous 03 Thickness_rh continuous 04 NPStest continuous 0Continuous Factors: Mean: StdDev:--- - --- Thickness_lh 2.643 0.116 Thickness_rh 2.630 0.099 NPStest 0.774 1.203Number of subjects: 31Number of factors:4 (1 discrete, 3 continuous)Number of classes:2Number of regressors: 8NPStest is scored from 0 to 8 and for controls it is all 0.Previously I have performed qdec without problem but I'm noting that when I use covariates that contains all 0 in a group, qdec give me an error. What's happen?Thanks, Stefano ___ 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] Bug in DOSS implementation in QDEC
On 03/25/2013 02:09 PM, Douglas N Greve wrote: Dear FreeSurferers, it has just come to my attention that there may be a bug in the way that QDEC computes contrasts for DOSS. If you are using QDEC in this way, please hold off until I track down the problem. Also, please let me know if you are using it in this way. thanks and sorry for the inconvenience doug Douglas: what do freesurfer version is affect? attachment: jm.vcf___ 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] Incorporating (high resolution) T2- and FLAIR volumes
1a) You would do this after running recon-all on the T1-weighted image. It will only adjust the surfaces, not the segmentation. Something like recon-all -T2pial path to flair 1b) this will work with either, but in my experience the FLAIR helps more to distinguish dura from gm 2) Yes. The standard aseg will label them and we have some custom tools that are more accurate if you have other image contrasts. I don't think they are quite distributed yet, but perhaps Doug can comment. 3) Sure, this isn't too hard. David Salat has published using the gray/white ratio as an interesting biomarker and the techniques would be pretty similar. I think Matt mostly used FreeSurfer for his analysis, but perhaps he can comment on the particulars cheers Bruce On Thu, 28 Mar 2013, lukas.sch...@ukb.uni-bonn.de wrote: Hi FreeSurfer experts! We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be fine to use the T2 / FLAIR volumes to improve the segmentation and to perform a couple additional analyses using FS. This leads to the following questions: 1) How do I incorporate T2/Flair volumes into the recon all processing stream? a) Would it be like: recon-all bert -all -T2 /luke/xyz/007-T2.nii ? b) What is expected to get the better results regarding the pial surface: FLAIR or T2? (both are at 1x1x1mm) 2) Is there any module in FS to detect white matter lesions? 3) How can I perform myelin mapping using the ratio method (T1w/T2w)? Or do I have to switch to Caret? Many thanks in advance for your help and advice! Best wishes, Luke ___ 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] Underestimated Pial surface - after deleting problematic voxels
eek, that's pretty bad. No idea why that would happen. Can you send us the recon-all.log? If you rerun with the original brain.finalsurfs.mgz does it restore good surfaces? On Thu, 28 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello Freesurfers, I ran recon-all on a subject's structural data like so: recon-all -autorecon-all -subjid subect_name The resulting pial surface looked pretty good except that there were a few voxels of dura and cerebellum that were included in the pial surface. not a big deal. I deleted some voxels of dura from brainmask.mgz and deleted voxels of from the cerebellum by creating and saving a copy of brain.finalsurfs.mgz. /subject_name/mri/ cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then I ran recon all to regenerate the pial surface: recon-all -autorecon-pial -subjid subject_name The results from the pial surface redrawing are now totally wrong and completely underestimated. The weird thing is that it looked perfectly fine before and removing some problematic voxels caused this result. Any insights as to how/why this occurred and how to fix it? Images of the AFTER picture attached. Thanks! -Ronny ___ 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] Underestimated Pial surface - after deleting problematic voxels
well, something is really wrong. Did you happen to change the voxel type of brain.finalsurfs.mgz? Can you run mri_info on it and send us the results? If not, then upload the tarred and gzipped subject dir and I'll take a look. I don't think it will be hard to fix On Thu, 28 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: A) Log attached. B) That was my next step but I wanted to check first to see if there was something obvious I was missing. I actually ran recon-all -autorecon-pial -subjid subject_name twice. I thought the first time, that it was the result of some process failing/not completing along the way without entirely crashing freesurfer. I ran it again in the hopes that it was some crazy fluke but the result is exactly the same. -Ronny eek, that's pretty bad. No idea why that would happen. Can you send us the recon-all.log? If you rerun with the original brain.finalsurfs.mgz does it restore good surfaces? On Thu, 28 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello Freesurfers, I ran recon-all on a subject's structural data like so: recon-all -autorecon-all -subjid subect_name The resulting pial surface looked pretty good except that there were a few voxels of dura and cerebellum that were included in the pial surface. not a big deal. I deleted some voxels of dura from brainmask.mgz and deleted voxels of from the cerebellum by creating and saving a copy of brain.finalsurfs.mgz. /subject_name/mri/ cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then I ran recon all to regenerate the pial surface: recon-all -autorecon-pial -subjid subject_name The results from the pial surface redrawing are now totally wrong and completely underestimated. The weird thing is that it looked perfectly fine before and removing some problematic voxels caused this result. Any insights as to how/why this occurred and how to fix it? Images of the AFTER picture attached. Thanks! -Ronny ___ 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] Underestimated Pial surface - after deleting problematic voxels
mri_info for both attached. Interestingly enough, brain.finalsurfs.manedit.mgz is significantly larger in size. If it was a copy of the other, shouldn't it be the same size? Also, brain.finalsurfs.manedit.mgz shows a time/date stamp from the last time I edited it and brain.finalsurfs.mgz has a time/date stamp from the last time I executed recon-all -autorecon-pial... -rw-rw-r-- 1 preciado birn 1416877 Mar 26 22:23 brain.finalsurfs.manedit.mgz -rw-rw-r-- 1 preciado birn16605 Mar 27 09:39 brain.finalsurfs.mgz A more basic question, I am assuming that -autorecon-pial defaults to using brain.finalsurfs.manedit.mgz and then proceeds to use brain.finalsurfs.mgz if there is no manual edit volume, is that correct? -Ronny well, something is really wrong. Did you happen to change the voxel type of brain.finalsurfs.mgz? Can you run mri_info on it and send us the results? If not, then upload the tarred and gzipped subject dir and I'll take a look. I don't think it will be hard to fix On Thu, 28 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: A) Log attached. B) That was my next step but I wanted to check first to see if there was something obvious I was missing. I actually ran recon-all -autorecon-pial -subjid subject_name twice. I thought the first time, that it was the result of some process failing/not completing along the way without entirely crashing freesurfer. I ran it again in the hopes that it was some crazy fluke but the result is exactly the same. -Ronny eek, that's pretty bad. No idea why that would happen. Can you send us the recon-all.log? If you rerun with the original brain.finalsurfs.mgz does it restore good surfaces? On Thu, 28 Mar 2013, preci...@nmr.mgh.harvard.edu wrote: Hello Freesurfers, I ran recon-all on a subject's structural data like so: recon-all -autorecon-all -subjid subect_name The resulting pial surface looked pretty good except that there were a few voxels of dura and cerebellum that were included in the pial surface. not a big deal. I deleted some voxels of dura from brainmask.mgz and deleted voxels of from the cerebellum by creating and saving a copy of brain.finalsurfs.mgz. /subject_name/mri/ cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then I ran recon all to regenerate the pial surface: recon-all -autorecon-pial -subjid subject_name The results from the pial surface redrawing are now totally wrong and completely underestimated. The weird thing is that it looked perfectly fine before and removing some problematic voxels caused this result. Any insights as to how/why this occurred and how to fix it? Images of the AFTER picture attached. Thanks! -Ronny brain.finalsurfs.mgz.mri_info Description: Binary data brain.finalsurfs.manedit.mgz.mri_info Description: Binary data ___ 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] Recon-all errors (reposting)
Hi, freesurferers I am trying to execute the post installation tests as recommended at Freesurfer Wiki. Using a CentOS6 Virtual Machine (kernel 2.6.32-358.2.1.el6.x86_64) over Fedora 18 using VirtualBox 4.2.8. Freesurfer version is 5.2. Tkmedit, Tksurfer, qdec and freeview all work great. However, recon-all tests return errors. Thank you for your attention. ___ recon-all -s bert -autorecon1 running loop to estimate saturation parameter: A or b constain NAN or infinity values!! ___ recon-all -s bert -all talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log ___ The log indicated above shows: imgrege: no voxels in register ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted ___ 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] Bug in DOSS implementation in QDEC
All versions are affected. doug On 03/28/2013 08:34 AM, jm wrote: On 03/25/2013 02:09 PM, Douglas N Greve wrote: Dear FreeSurferers, it has just come to my attention that there may be a bug in the way that QDEC computes contrasts for DOSS. If you are using QDEC in this way, please hold off until I track down the problem. Also, please let me know if you are using it in this way. thanks and sorry for the inconvenience doug Douglas: what do freesurfer version is affect? ___ 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 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.
Re: [Freesurfer] Incorporating (high resolution) T2- and FLAIR volumes
I find the T2w image works well for removing dura and blood vessels, but I'm not sure FLAIR would work for T1w/T2w myelin mapping because of what would happen to the ratio near the pial surface. Instructions for T1w/T2w myelin mapping are available here: http://brainvis.wustl.edu/wiki/index.php/Caret:MyelinMaps One starts with FreeSurfer outputs. Bruce: do you guys have an unsmoothed group average grey/white map? We could do a quick comparison on fsaverage if you guys were interested. Peace, Matt. On 3/28/13 7:45 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: 1a) You would do this after running recon-all on the T1-weighted image. It will only adjust the surfaces, not the segmentation. Something like recon-all -T2pial path to flair 1b) this will work with either, but in my experience the FLAIR helps more to distinguish dura from gm 2) Yes. The standard aseg will label them and we have some custom tools that are more accurate if you have other image contrasts. I don't think they are quite distributed yet, but perhaps Doug can comment. 3) Sure, this isn't too hard. David Salat has published using the gray/white ratio as an interesting biomarker and the techniques would be pretty similar. I think Matt mostly used FreeSurfer for his analysis, but perhaps he can comment on the particulars cheers Bruce On Thu, 28 Mar 2013, lukas.sch...@ukb.uni-bonn.de wrote: Hi FreeSurfer experts! We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be fine to use the T2 / FLAIR volumes to improve the segmentation and to perform a couple additional analyses using FS. This leads to the following questions: 1) How do I incorporate T2/Flair volumes into the recon all processing stream? a) Would it be like: recon-all bert -all -T2 /luke/xyz/007-T2.nii ? b) What is expected to get the better results regarding the pial surface: FLAIR or T2? (both are at 1x1x1mm) 2) Is there any module in FS to detect white matter lesions? 3) How can I perform myelin mapping using the ratio method (T1w/T2w)? Or do I have to switch to Caret? Many thanks in advance for your help and advice! Best wishes, Luke ___ 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] Antwort: Re: Incorporating (high resolution) T2- and FLAIR volumes
Dear Matt! Thanks a lot. We do have both FLAIR and T2 - so I could use the FLAIR for the clean-up procedure and use the T2 volumes for myelin part... Best wishes, Luke Matt Glasser m...@ma-tea.com An 28.03.2013 15:37 Bruce Fischl fis...@nmr.mgh.harvard.edu, lukas.sch...@ukb.uni-bonn.de Kopie freesurfer@nmr.mgh.harvard.edu Thema Re: [Freesurfer] Incorporating (high resolution) T2- and FLAIR volumes I find the T2w image works well for removing dura and blood vessels, but I'm not sure FLAIR would work for T1w/T2w myelin mapping because of what would happen to the ratio near the pial surface. Instructions for T1w/T2w myelin mapping are available here: http://brainvis.wustl.edu/wiki/index.php/Caret:MyelinMaps One starts with FreeSurfer outputs. Bruce: do you guys have an unsmoothed group average grey/white map? We could do a quick comparison on fsaverage if you guys were interested. Peace, Matt. On 3/28/13 7:45 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: 1a) You would do this after running recon-all on the T1-weighted image. It will only adjust the surfaces, not the segmentation. Something like recon-all -T2pial path to flair 1b) this will work with either, but in my experience the FLAIR helps more to distinguish dura from gm 2) Yes. The standard aseg will label them and we have some custom tools that are more accurate if you have other image contrasts. I don't think they are quite distributed yet, but perhaps Doug can comment. 3) Sure, this isn't too hard. David Salat has published using the gray/white ratio as an interesting biomarker and the techniques would be pretty similar. I think Matt mostly used FreeSurfer for his analysis, but perhaps he can comment on the particulars cheers Bruce On Thu, 28 Mar 2013, lukas.sch...@ukb.uni-bonn.de wrote: Hi FreeSurfer experts! We have isotropic T1/T2 and FLAIR volumes for a larger cohort. It would be fine to use the T2 / FLAIR volumes to improve the segmentation and to perform a couple additional analyses using FS. This leads to the following questions: 1) How do I incorporate T2/Flair volumes into the recon all processing stream? a) Would it be like: recon-all bert -all -T2 /luke/xyz/007-T2.nii ? b) What is expected to get the better results regarding the pial surface: FLAIR or T2? (both are at 1x1x1mm) 2) Is there any module in FS to detect white matter lesions? 3) How can I perform myelin mapping using the ratio method (T1w/T2w)? Or do I have to switch to Caret? Many thanks in advance for your help and advice! Best wishes, Luke ___ 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. inline: graycol.gifinline: pic02341.gifinline: ecblank.gif___ 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] Problem with tracula: incomplete or lacking tracts
Hi Stefano - Nothing has changed with these variables between 5.1 and 5.2. So do with them whatever you were doing before. a.y On Thu, 28 Mar 2013, std...@virgilio.it wrote: Hi Analstasia, as you suggest, adjusting brain mask the tracts are better. Now I'd like to perform trac-all with new version by using a new configuration file. I do not understand what I should do for: 1- set b0mlist 2- set b0plist Thanks. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 20.22 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: Problem with tracula: incomplete or lacking tracts Yes, it's a warning, not an error. On Mon, 25 Mar 2013, std...@virgilio.it wrote: Hi Anastasia,now I have correct the nodif mask and run again trac-all. Is normal WARN: Could not find satisfactory control point fit - try 83Finding center streamline during -prior? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 18.02 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts I also remember that your brain masks had some big chunks of brain missing. Was whatever caused that fixed as well? On Mon, 25 Mar 2013, std...@virgilio.it wrote: Yes, I fix them. I'm attacking the maps after the last trac-all. Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 25-mar-2013 17.26 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - As I recall, we established that your bvecs were wrong. Did you fix them? a.y On Mon, 25 Mar 2013, std...@virgilio.it wrote: Hi Anastasia, I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends from an error in my configuration file? I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? Thanks, Stefano On Fri, 22 Mar 2013, std...@virgilio.it wrote: Thank you Anastasia. I'm checking bvecs/bvals. I obtain it by DTI table creator (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) bvecs/bvals should be done. Gradients can be the unique responsable? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 17.07 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Your gradient table is wrong. See where I've marked the corpus callosum in your screenshot. The eigenvectors are not pointing along the corpus callosum, but perpendicular to it. So they're off by 90 degrees, which means the same is true about the vectors in your gradient table. On Fri, 22 Mar 2013, std...@virgilio.it wrote: Hi Anastasia - I attacked the screenshots. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 22-mar-2013 1.39 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts Hi Stefano - There's nothing in these screenshots that tells you that the eigenvectors are correct. These are vectors, so the way to check them is to display them as lines. You display dtifit_V1 as lines, overlaid on dtifit_FA. Then you see if the lines point in the right direction. a.y On Fri, 22 Mar 2013, std...@virgilio.it wrote: Here they are attacked. Thanks, Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 21-mar-2013 21.50 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts Can you send a screenshot that shows dtifit_V1 and dtifit_FA? On Thu, 21 Mar 2013, std...@virgilio.it wrote: I have checked the gradient directions. How can I resolve the brain mask problem. Can I send you my files of this subject? Stefano Messaggio originale Da: ayend...@nmr.mgh.harvard.edu Data: 20-mar-2013 22.46 A: std...@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts There are chunks of the brain missing from the brain mask. This may cause some tracts to be incomplete or missing. But you should still check
Re: [Freesurfer] error during trac-all -prep
Hi Jon - The command that fails is trying to multiply 2 volumes and complains that they have different sizes. Have you checked if these 2 volumes exist and what their dimensions are? a.y On Wed, 27 Mar 2013, Jon Wieser wrote: i ran trac-all -prep -c dmrirc_single_subject and got the error : fslmaths /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask.nii.gz -mul /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/notventricles.nii.gz /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask-vent.nii.gz Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort I have attached the trac-all .log and trac-all.error files I don't know how to fix this error Thanks Jon ___ 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] Different MPRAGE sequences
Hello list, I have a group of subjects (4 patients and 8 controls) in which one MPRAGE sequence was used and another group of subjects (2 patients and 2 controls) where a diffent MPRAGE was used. Both groups were acquired in the same scanner. For each subject I have two anatomical sequences and I'm working with the average dataset. My question is can I put both groups together for comparision? I've thought about this and I can't really be sure... I was thinking that since for group 2 the number of acquisitions is balanced maybe the overall impact of different sequences won't be significative... Patients and subjects are age-matched in both groups. Please, any advice will be greatly appreciated! Thank you! ___ 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] trac-all -path error
Hi Nawaf - Can you please send your trac-all.log? It's possible that the problem started at an earlier step. Thanks, a.y On Thu, 28 Mar 2013, Nawaf Yassi wrote: Dear mailing list I am encountering an error at the trac-all –path stage of a tracula analysis (the first two stages on trac-all seem to have run ok) with the appropriate outputs. I am getting the error “Segmentation fault” (core dumped) very early on after the dmri_paths command is run (see below). Can anyone help? I am using freesurfer 5.2 and FSL 5.0.2.1 (linux) Regards Nawaf ATTACHED: ERROR MESSAGE + config file below = [nyassi@bee1 scripts]$ trac-all -path -c dmrirc_single_subject Too many )'s. INFO: SUBJECTS_DIR is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer INFO: Diffusion root is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer Actual FREESURFER_HOME /usr/local/freesurfer5.2 trac-paths -c/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/scripts/ dmrirc.local -log/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/scripts/ trac-all.log -cmd/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/scripts/ trac-all.cmd #- /usr/local/freesurfer5.2/bin/trac-paths #- #@# Path reconstruction Thu Mar 28 10:01:34 EST 2013 rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .cst_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .cst_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .ilf_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .ilf_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .unc_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .unc_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm ajor_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm inor_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .atr_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .atr_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .ccg_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .ccg_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .cab_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .cab_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .slfp_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .slfp_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .slft_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .slft_PP_avg33_mni_bbr /usr/local/freesurfer5.2/bin/dmri_paths --outdir/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm ajor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm inor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .atr_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .atr_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .ccg_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .ccg_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh
Re: [Freesurfer] Tracula Cluster Question
Hi Sal, 1. I have no experience with the sun grid engine, perhaps someone else on the list can help with that. 2. The -bedp step needs the outputs from the -corr and -masks steps. The -path step needs the outputs from the -bedp step. The output files from each part are listed here: http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles 3. Checking the aparc+aseg should be enough for tracula purposes as well, since that's the freesurfer output that tracula uses. Keep in mind that DWI resolution is usually lower than T1 resolution, so tiny changes in the aparc+aseg might not affect tracula at all. 4. Yes, I do recommend using bbregister. It's not surprising that it would give better results since it uses the additional information of the surfaces. If I remember correctly, Doug didn't manage to replicate your bbregister error, right? I'd check if you get the same error with the 5.1 version of bbregister. Hope this helps, a.y On Wed, 27 Mar 2013, Salil Soman wrote: Hi, I have been able to implement FS 5.2 on our Sun Grid Engine Cluster using the CentOS 6 distribution. After modifying the fsl_sub_mgh file to work with out cluster queue names and to modify the email notifications, I am able to run the entire processing pipeline using FLT. (Everytime I try bbr I get errors. I had email doug about this but have not heard any response). I am submitting the jobs to the cluster as follows recon-all -i ./*.nii -s WCA_0202_T1_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all trac-all -prep -no-isrunning -c /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc trac-all -bedp -no-isrunning -c /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc trac-all -path -no-isrunning -c /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc There are a few issues I am trying to sort out: 1) how should one conifigure the openmp flag for the Sun Grid Engine? the flag I used did not change processing time, and each subject is still taking ~24 hrs? 2) once the script starts bedpost, bedpost has controller code which paralelizes all of the slices (which has been great going from 12 hrs of processing to 1.5 hrs). However, my original script goes on to execute trace-all -path ... before bepost is done, generating errors. I have gotten around this by running the trace-all -path command again after bedpost sends me an email confirming completion. Is there a way to more cleanly do this (some kind of hold command I can do based on output from bedpost)? 3) In your experience, how important is quality control of freesurfer on tracula results? We have come to the compromise for freesurfer output to manually check the segmentation of aparc+aseg.mgz using free view, only correcting and rerunning steps of freesurfer when there are specific structures we want the volumes of (eg hippocampus). 4) have you found a significant benefit of bbr over flt? If so, any suggestions on things I may need to check to get bbr to work (given flt works)? Best wishes, Sal ___ 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 during trac-all -prep
You can open them in a viewer, or just run mri_info on them. On Thu, 28 Mar 2013, Jon Wieser wrote: How do i check the dimensions of the volumes? Jon - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Jon Wieser wie...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Thursday, March 28, 2013 10:13:19 AM Subject: Re: [Freesurfer] error during trac-all -prep Hi Jon - The command that fails is trying to multiply 2 volumes and complains that they have different sizes. Have you checked if these 2 volumes exist and what their dimensions are? a.y On Wed, 27 Mar 2013, Jon Wieser wrote: i ran trac-all -prep -c dmrirc_single_subject and got the error : fslmaths /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask.nii.gz -mul /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/notventricles.nii.gz /BrainLabDocs/Studies/Alcohol_Study/Alc_Data_Faces/1223/freesurfer/dlabel/anatorig/anat_brain_mask-vent.nii.gz Image Exception : #3 :: Attempted to multiply images/ROIs of different sizes terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort I have attached the trac-all .log and trac-all.error files I don't know how to fix this error Thanks Jon 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] memory allocation errors on Snow Leopard running dmri_train (fwd)
Hi Ping - It'll make it easier for us to replicate your memory error if you send us the data set where you get the error. Can you please zip up the dmri, dmri.bedpostX, and dlabel directories for this subject and upload them for me and Zeke? https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks, a.y On Wed, 27 Mar 2013, Ping-Hong Yeh wrote: Hi Zeke, That specific subject had v5.1 recon-all run by Leopard with FS v5.1 (another computer), but v5.2 trac-all run by Snow Leopard with FS v5.2 . If you scroll down the log file, you will see the /Application/freesurfer, which is the v5.2 where it crashed. Anyhow I have attached the log file of another subject run by FS 5.2, both recon-all and trac-all. Thanks. ping On Wed, Mar 27, 2013 at 4:00 PM, zkauf...@nmr.mgh.harvard.edu zkauf...@nmr.mgh.harvard.edu wrote: Ping, According to line 9 of the log file you sent to Anastasia, are running freesurfer version v5.1. Not version 5.2. -Zeke Original Message Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train (fwd) Date: Wed, 27 Mar 2013 15:17:34 -0400 (EDT) From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: Zeke Kaufman zkauf...@nmr.mgh.harvard.edu -- Forwarded message -- Date: Wed, 27 Mar 2013 13:44:56 -0400 From: Ping-Hong Yeh pinghong...@gmail.com To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] memory allocation errors on Snow Leopard running dmri_train Hi Anastasia, See the attached. Thank you. ping On Wed, Mar 27, 2013 at 1:38 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Can you send us your entire trac-all.log? There's some info in there about your system and the freesurfer build you're using that we'll need to try to replicate the problem. Thanks, a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi Anastasia, It had the same issue before, but worked fine after installing the fixed dmri patch for Snow Leopard. Thanks. ping On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz
[Freesurfer] mris_thickness qcache for xhemi surfaces
Dear Freesurfer experts, I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. In my lab we generally process ?h.thickness files with the next two commands before statistically analysis: mris_thickness -max 10 subjid ?h thickness_max10 recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h To keep with this protocol, my questions are 1) how do I use mris_thickness properly so that I don't overwrite the files registered to fsaverage_510? 2) in recon-all -qcache, will it do the trick by substituting fsaverage_sym for fsaverage_510? Thank you in advance, Cherry ___ 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] Different MPRAGE sequences
it really depends on what the differences are. The best thing to do would be to scan some controls with both sequences and see what the differences are, although that won't rule out some disease-specific differences that you only see in the patients On Thu, 28 Mar 2013, _andre...@sapo.pt wrote: Hello list, I have a group of subjects (4 patients and 8 controls) in which one MPRAGE sequence was used and another group of subjects (2 patients and 2 controls) where a diffent MPRAGE was used. Both groups were acquired in the same scanner. For each subject I have two anatomical sequences and I'm working with the average dataset. My question is can I put both groups together for comparision? I've thought about this and I can't really be sure... I was thinking that since for group 2 the number of acquisitions is balanced maybe the overall impact of different sequences won't be significative... Patients and subjects are age-matched in both groups. Please, any advice will be greatly appreciated! Thank you! ___ 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] Different MPRAGE sequences
p.s. you would be better off if you had the same proportion of patients and controls with each sequence. Matching the numbers within one sequence and not the other doesn't really help On Thu, 28 Mar 2013, _andre...@sapo.pt wrote: Hello list, I have a group of subjects (4 patients and 8 controls) in which one MPRAGE sequence was used and another group of subjects (2 patients and 2 controls) where a diffent MPRAGE was used. Both groups were acquired in the same scanner. For each subject I have two anatomical sequences and I'm working with the average dataset. My question is can I put both groups together for comparision? I've thought about this and I can't really be sure... I was thinking that since for group 2 the number of acquisitions is balanced maybe the overall impact of different sequences won't be significative... Patients and subjects are age-matched in both groups. Please, any advice will be greatly appreciated! Thank you! ___ 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] Different MPRAGE sequences
Hi Bruce, I did that test some time ago (each sequence alone or averaged) but only with one control subject. I then checked the values of different measures and the cortical thickness maps for each situation and they were very similar indeed. I did it only with one subject because the point was to choose one of the MPRAGEs. But now that I need to drag conclusions I wasn't sure if the different sequences would be a major problem and would invalidate the conclusions. I'll match the number of subjects for each sequence but bearing in mind that I have two different sequences anyway. Thank you for the help! Andreia Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu: p.s. you would be better off if you had the same proportion of patients and controls with each sequence. Matching the numbers within one sequence and not the other doesn't really help On Thu, 28 Mar 2013, _andre...@sapo.pt wrote: Hello list, I have a group of subjects (4 patients and 8 controls) in which one MPRAGE sequence was used and another group of subjects (2 patients and 2 controls) where a diffent MPRAGE was used. Both groups were acquired in the same scanner. For each subject I have two anatomical sequences and I'm working with the average dataset. My question is can I put both groups together for comparision? I've thought about this and I can't really be sure... I was thinking that since for group 2 the number of acquisitions is balanced maybe the overall impact of different sequences won't be significative... Patients and subjects are age-matched in both groups. Please, any advice will be greatly appreciated! Thank you! ___ 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] perirhinal analysis
It says no such file or directory does rh.perifhyinal.label exist? On 03/28/2013 11:55 AM, std...@virgilio.it wrote: Hi list, I'm running perirhinal analysis with this error: mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi rh --regmethod surface srclabel = rh.perirhinal.label srcsubject = fsaverage trgsubject = Con01 trglabel = Con01/label/rh.perirhinal.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file rh.perirhinal.label No such file or directory ERROR reading rh.perirhinal.label My $SUBJECTS_DIR=/Applications/freesurfer/subjects/subject_prova and rh.perirhinal.label exist and it is located in /Applications/freesurfer/subjects/subject_prova/Con01/label Thanks, 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: 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.
Re: [Freesurfer] mris_thickness qcache for xhemi surfaces
On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: Dear Freesurfer experts, I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. In my lab we generally process ?h.thickness files with the next two commands before statistically analysis: mris_thickness -max 10 subjid ?h thickness_max10 recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h To keep with this protocol, my questions are 1) how do I use mris_thickness properly so that I don't overwrite the files registered to fsaverage_510? I think it will recreate the basic ?h.thickness file and will not touch registrations. 2) in recon-all -qcache, will it do the trick by substituting fsaverage_sym for fsaverage_510? Yes, that should work. Thank you in advance, Cherry ___ 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 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.
Re: [Freesurfer] mris_thickness qcache for xhemi surfaces
Actually, #2 will not work. I don't think you can use qdec with the xhemi stuff anyway. You should use the mris_preproc command followed by mri_glmfit. doug On 03/28/2013 12:51 PM, Douglas N Greve wrote: On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: Dear Freesurfer experts, I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. In my lab we generally process ?h.thickness files with the next two commands before statistically analysis: mris_thickness -max 10 subjid ?h thickness_max10 recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h To keep with this protocol, my questions are 1) how do I use mris_thickness properly so that I don't overwrite the files registered to fsaverage_510? I think it will recreate the basic ?h.thickness file and will not touch registrations. 2) in recon-all -qcache, will it do the trick by substituting fsaverage_sym for fsaverage_510? Yes, that should work. Thank you in advance, Cherry ___ 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 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] Set up data for longitudinal processing
Hi folks, sorry it's me again with a very basic question. What is the best way to import longitudinal data? recon-all -i /path/T1A.nii -i /path/T1B.nii FIRSTSUBJECT or recon-all -i /path/T1A.nii FIRSTSUBJECT_A recon-all -i /path/T1A.nii FIRSTSUBJECT_B I tend to use the second choice because otherwise I would have no idea how to distinguish between SUBJECT-ID and TimepointID later on in the processing stream. Best whises, Luke___ 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] mris_thickness qcache for xhemi surfaces
Thanks, Doug. I'm not planning to use qdec. It's just that I used to generate the ?h.thickness_max10.fwhm10.fsaverage_510.mgh files (which are what we name the files after running the two commands) before I use mris_preproc and mri_glmfit. I also generally skip the smooth step in freesurfer tutorial since the files are smoothed in the first place. Any suggestions? Cherry On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Actually, #2 will not work. I don't think you can use qdec with the xhemi stuff anyway. You should use the mris_preproc command followed by mri_glmfit. doug On 03/28/2013 12:51 PM, Douglas N Greve wrote: On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: Dear Freesurfer experts, I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. In my lab we generally process ?h.thickness files with the next two commands before statistically analysis: mris_thickness -max 10 subjid ?h thickness_max10 recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h To keep with this protocol, my questions are 1) how do I use mris_thickness properly so that I don't overwrite the files registered to fsaverage_510? I think it will recreate the basic ?h.thickness file and will not touch registrations. 2) in recon-all -qcache, will it do the trick by substituting fsaverage_sym for fsaverage_510? Yes, that should work. Thank you in advance, Cherry ___ 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 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] Set up data for longitudinal processing
Hi Luke if I understand you properly the second way it the correct way (assuming T1A.nii and T1b.nii are two timepoints for a subject). I think you have a typo though as your second recon-all should use T1B.nii as input. cheers Bruce On Thu, 28 Mar 2013, lukas.sch...@ukb.uni-bonn.de wrote: Hi folks, sorry it's me again with a very basic question. What is the best way to import longitudinal data? recon-all -i /path/T1A.nii -i /path/T1B.nii FIRSTSUBJECT or recon-all -i /path/T1A.nii FIRSTSUBJECT_A recon-all -i /path/T1A.nii FIRSTSUBJECT_B I tend to use the second choice because otherwise I would have no idea how to distinguish between SUBJECT-ID and TimepointID later on in the processing stream. Best whises, Luke ___ 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] mris_thickness qcache for xhemi surfaces
Hi Cherry, what I meant was that you cannot use the qcache with xhemi. You'll need to run the mris_preproc command as listed on the web page. doug On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote: Thanks, Doug. I'm not planning to use qdec. It's just that I used to generate the ?h.thickness_max10.fwhm10.fsaverage_510.mgh files (which are what we name the files after running the two commands) before I use mris_preproc and mri_glmfit. I also generally skip the smooth step in freesurfer tutorial since the files are smoothed in the first place. Any suggestions? Cherry On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Actually, #2 will not work. I don't think you can use qdec with the xhemi stuff anyway. You should use the mris_preproc command followed by mri_glmfit. doug On 03/28/2013 12:51 PM, Douglas N Greve wrote: On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: Dear Freesurfer experts, I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. In my lab we generally process ?h.thickness files with the next two commands before statistically analysis: mris_thickness -max 10 subjid ?h thickness_max10 recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h To keep with this protocol, my questions are 1) how do I use mris_thickness properly so that I don't overwrite the files registered to fsaverage_510? I think it will recreate the basic ?h.thickness file and will not touch registrations. 2) in recon-all -qcache, will it do the trick by substituting fsaverage_sym for fsaverage_510? Yes, that should work. Thank you in advance, Cherry ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center 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 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] R: Re: perirhinal analysis
Yes, it is located in /Applications/freesurfer/subjects/subject_prova/Con01/label/rh.perirhinal.label. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 28-mar-2013 17.46 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] perirhinal analysis It says no such file or directory does rh.perifhyinal.label exist? On 03/28/2013 11:55 AM, std...@virgilio.it wrote: Hi list, I'm running perirhinal analysis with this error: mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi rh --regmethod surface srclabel = rh.perirhinal.label srcsubject = fsaverage trgsubject = Con01 trglabel = Con01/label/rh.perirhinal.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /Applications/freesurfer/subjects/subject_prova FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file rh.perirhinal.label No such file or directory ERROR reading rh.perirhinal.label My $SUBJECTS_DIR=/Applications/freesurfer/subjects/subject_prova and rh.perirhinal.label exist and it is located in /Applications/freesurfer/subjects/subject_prova/Con01/label Thanks, 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: 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] mris_thickness qcache for xhemi surfaces
I see. Then I think I'd better just follow the instructions on the Xhemi page. Thanks! On Thu, Mar 28, 2013 at 1:06 PM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Hi Cherry, what I meant was that you cannot use the qcache with xhemi. You'll need to run the mris_preproc command as listed on the web page. doug On 03/28/2013 01:00 PM, Ejoe Yizhou Ma wrote: Thanks, Doug. I'm not planning to use qdec. It's just that I used to generate the ?h.thickness_max10.fwhm10.**fsaverage_510.mgh files (which are what we name the files after running the two commands) before I use mris_preproc and mri_glmfit. I also generally skip the smooth step in freesurfer tutorial since the files are smoothed in the first place. Any suggestions? Cherry On Thu, Mar 28, 2013 at 12:53 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu wrote: Actually, #2 will not work. I don't think you can use qdec with the xhemi stuff anyway. You should use the mris_preproc command followed by mri_glmfit. doug On 03/28/2013 12:51 PM, Douglas N Greve wrote: On 03/28/2013 12:16 PM, Ejoe Yizhou Ma wrote: Dear Freesurfer experts, I'm trying to investigate lh-to-rh asymmetry, so I register my subjects to the subject of fsaverage_sym following the instructions on this page: http://surfer.nmr.mgh.harvard.**edu/fswiki/Xhemihttp://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi . After all the surfreg commands I've got ?h.thickness files in subjid/xhemi/surf. In my lab we generally process ?h.thickness files with the next two commands before statistically analysis: mris_thickness -max 10 subjid ?h thickness_max10 recon-all -qcache -measure thickness_max10 -target fsaverage_510 -fwhm 10 -no-isrunning -s subjid -hemi ?h To keep with this protocol, my questions are 1) how do I use mris_thickness properly so that I don't overwrite the files registered to fsaverage_510? I think it will recreate the basic ?h.thickness file and will not touch registrations. 2) in recon-all -qcache, will it do the trick by substituting fsaverage_sym for fsaverage_510? Yes, that should work. Thank you in advance, Cherry __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** greve/ ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Re: [Freesurfer] R: Re: perirhinal analysis
If the source subject is subject_prova then you need to spec that subjet 2with --srcsubject (instead of fsaverage) doug On 03/28/2013 01:11 PM, std...@virgilio.it wrote: Yes, it is located in /Applications/freesurfer/subjects/subject_prova/Con01/label/rh.perirhinal.label. Stefano Messaggio originale Da: gr...@nmr.mgh.harvard.edu Data: 28-mar-2013 17.46 A: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] perirhinal analysis It says no such file or directory does rh.perifhyinal.label exist? On 03/28/2013 11:55 AM, std...@virgilio.it wrote: Hi list, I'm running perirhinal analysis with this error: mri_label2label --srcsubject fsaverage --srclabel rh.perirhinal.label --trgsubject Con01 --trglabel Con01/label/rh.perirhinal.label --hemi rh --regmethod surface srclabel = rh.perirhinal.label srcsubject = fsaverage trgsubject = Con01 trglabel = Con01/label/rh.perirhinal.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova FREESURFER_HOME /Applications/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file rh.perirhinal.label No such file or directory ERROR reading rh.perirhinal.label My $SUBJECTS_DIR=/Applications/freesurfer/subjects/subject_prova and rh.perirhinal.label exist and it is located in /Applications/freesurfer/subjects/subject_prova/Con01/label Thanks, 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: 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. -- 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 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] spmregister error
Hi Freesurfers, I'm in the middle of coregistering a CT and MRI, and after running spmregister --s MGXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig I get the error that orig.mgz is not found in COR or MGZ formats, but I have an orig.mgz file in my folder. Any help on this would be awesome! Thanks, Mia ___ 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] aseg.mgz altered after auto-recon2?
Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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] spmregister error
Make sure that there is an orig.mgz in $SUBJECTS_DIR/MGXX_SurferOutput/mri Also, make sure to send the full terminal output doug On 03/28/2013 02:13 PM, Borzello, Mia wrote: Hi Freesurfers, I'm in the middle of coregistering a CT and MRI, and after running spmregister --s MGXX_SurferOutput --mov ct.mgz --reg spm.reg.dat --fsvol orig I get the error that orig.mgz is not found in COR or MGZ formats, but I have an orig.mgz file in my folder. Any help on this would be awesome! Thanks, Mia ___ 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 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.
Re: [Freesurfer] aseg.mgz altered after auto-recon2?
In fact, couldn't I stop after calabel if all I want is the aseg.mgz? - Josh On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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] aseg.mgz altered after auto-recon2?
Hi Josh, yes, I think that's correct. Bruce On Thu, 28 Mar 2013, Joshua Lee wrote: In fact, couldn't I stop after calabel if all I want is the aseg.mgz? - Josh On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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] FSFAST and octave error dfor fast_selxavg3.m
Hi Freesurfer group, Im attempting to use FS-FAST with resting BOLD data, and I have come across the following error. I tried changing files to non .gz extension, and still have this error.. $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ `fast_selxavg3' is a script from the file /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m `fast_ldanaflac' is a function from the file /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m - outtop = /media/GOLDIN/FSFAST Extension format = nii.gz error: `MRIread' undefined near line 87 column 7 error: called from: error: /usr/local/freesurfer/fsfast/toolbox/flac_customize.m at line 87, column 5 error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 65, column 7 -- When I attempt to use fast_selxavg3 standalone in octave, I get this error. octave:1 fast_selxavg3; error: `sess' undefined near line 26 column 19 error: evaluating argument list element number 1 error: evaluating argument list element number 1 error: called from: error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line 26, column 8 thanks, Mario Ortega GS4 Washington University in St. Louis, Dept. of Neurology ___ 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 from mri_concat while using QDEC
Still stuck with this error in my QDEC analysis attempt, at my wit's end, could anyone help please? Thanks! Tudor On 26 March 2013 20:35, Tudor Popescu tud...@gmail.com wrote: Just giving this thread a new bump, as *again *I am receiving this error from mri_concat, upon pressing the Analyze button in QDEC. Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and includes a copy of the fsaverage folder) and all files included in the error are at the expected path. Screenshot attached. On 18 March 2013 11:20, Tudor Popescu tud...@gmail.com wrote: Hi Andreas I don't think it's about the OS (I'm on WInXP SP3, 32 bit, hosting Linux using Vritualbox), but about the environment variables, even though from what I could see, I had them all correctly set. I gave up and am just running this through FSL.. Tudor On 18 March 2013 11:13, Andreas Berger n0642...@students.meduniwien.ac.at wrote: On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: Hi Doug Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a \ at the end of my command, just after the file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. Also, the Analyze in the QDEC GUI now completes without error as well. It's quite frustrating that I still don't know why it hasn't been working all this time, especially since I didn't really do anything different now (that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder). Anyhow, thanks again for your kind help! Tudor On 31 January 2013 20:36, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: On 01/31/2013 12:30 PM, Tudor Popescu wrote: Hi Doug, I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file? Sorry, I did not mean to imply that the command line was wrong, rather that the behavior did not make sense -- it should print *something* to the terminal. It does make sense to have multiple files, but it will also work with a single file. I just suggested this to make things simpler. Anyway, after trying out the command with only one of the files from the tutorial, /mri_concat --debug /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* *thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/** subjects/qdec/y.mgh/ ..the same thing happens, namely it returns to the command prompt, with no message whatsoever. What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help! What happens if you type mri_concat with no options at all? Tudor On 20 December 2012 05:24, Douglas Greve gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu wrote: That does not make sense. Try using only one input file. Also, put --debug as the first option. doug On 12/19/12 8:32 AM, Tudor Popescu wrote: Hi Doug, So the full command is mri_concat /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/049/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/141/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/084/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/021/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/093/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/080/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/091/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/040/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/017/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/138/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/106/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/108/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/092/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/124/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/129/surf/lh.** thickness.fwhm10.fsaverage.mgh /media/Dell/_FS/buckner_data/**subjects/103/surf/lh.** thickness.fwhm10.fsaverage.mgh
Re: [Freesurfer] More QDEC questions
I was wondering if anybody is able to help with (any one of) these questions? That would be really helpful, as I could not find an answer on the wiki. Many thanks in advance! On 26 March 2013 20:44, Tudor Popescu tud...@gmail.com wrote: Hi everyone, My QDEC analysis ran into an error message that seems to be a classic (and, so far, it seems unsolved), from mri_concat, which I've described in a separate message, just sent. I have, however, more theoretical questions about QDEC, which I hope some kind soul will help me with: - why does QDEC only provide the volume of *subcortical* structures under StatsDataImport/aseg.volume, when the automatic GM/WM segmentation is done for the entire brain, not just for subcortical regions? - how are the volume measurements provided in aseg.volume different from the ones done obtained with a VBM analysis? - why is *volume *the result of *segmentation *(aseg.volume) whereas *thickness *derives from *parcelation *(rh.aparc.thickness)? Is it not the case that both operations (segmentation+parcellation) are necessary to calculate volume as well as thickness? - how is a QDEC thickness analysis different from a regular AN(C)OVA in which you are interested in main and interaction effects of the IVs on the DV? I ask this because some of the questions that appear in QDEC's Analysis Results tab – e.g. is the correlation between (DV) and (IV) different from zero? – would not (I think) be directly answerable by an ANOVA - would the same type of ANOVA done by QDEC be doable by extracting the values of the DV for each subject (using e.g. *aseg.volume*) and then doing the ANOVA in e.g. SPSS? If so, when would you do one versus the other? - why is it that only continuous factors (e.g. age) can be taken in the analysis as nuisance factors, when discrete variables (e.g. gender) might also be irrelevant for a particular analysis and thus belong to the Nuisance Factor list? Many thanks in advance!! Tudor ___ 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] aseg.mgz altered after auto-recon2?
Hi, Josh, I think you can run the autorecon1, subcortseg and no segstats if you don't want the statistics file (aseg.stats). Also, use -openmp 8 can speed up quite a lot by multi-threading. For a regular T1 brain image, I can the running time to get aseg.mgz in about 4-5 hours. recon-all -i subject autorecon1 -subcortseg -nosegstats -openmp 8 cheers, Natalie On Thu, Mar 28, 2013 at 12:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Josh, yes, I think that's correct. Bruce On Thu, 28 Mar 2013, Joshua Lee wrote: In fact, couldn't I stop after calabel if all I want is the aseg.mgz? - Josh On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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] FSFAST and octave error dfor fast_selxavg3.m
make sure to add the following lines to your ~/matlab/startup.m
FSH = getenv('FREESURFER_HOME');
fshmatlab = sprintf('%s/matlab',FSH);
path(path,fshmatlab);
clear fshmatlab FSH;
doug
On 03/28/2013 03:48 PM, Mario Ortega wrote:
Hi Freesurfer group, Im attempting to use FS-FAST with resting BOLD
data, and I have come across the following error.
I tried changing files to non .gz extension, and still have this error..
$Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $
`fast_selxavg3' is a script from the file
/usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
`fast_ldanaflac' is a function from the file
/usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
-
outtop = /media/GOLDIN/FSFAST
Extension format = nii.gz
error: `MRIread' undefined near line 87 column 7
error: called from:
error: /usr/local/freesurfer/fsfast/toolbox/flac_customize.m at line
87, column 5
error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line
65, column 7
--
When I attempt to use fast_selxavg3 standalone in octave, I get this
error.
octave:1 fast_selxavg3;
error: `sess' undefined near line 26 column 19
error: evaluating argument list element number 1
error: evaluating argument list element number 1
error: called from:
error: /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m at line
26, column 8
thanks,
Mario Ortega
GS4 Washington University in St. Louis, Dept. of Neurology
___
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--
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
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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 from mri_concat while using QDEC
Sorry, I've totally lost track of this thread. Are you able to run mri_concat outside of QDEC? On 03/28/2013 03:51 PM, Tudor Popescu wrote: Still stuck with this error in my QDEC analysis attempt, at my wit's end, could anyone help please? Thanks! Tudor On 26 March 2013 20:35, Tudor Popescu tud...@gmail.com mailto:tud...@gmail.com wrote: Just giving this thread a new bump, as /again /I am receiving this error from mri_concat, upon pressing the Analyze button in QDEC. Usual suspects are ruled out: $SUBJECTS_DIR is set correctly (and includes a copy of the fsaverage folder) and all files included in the error are at the expected path. Screenshot attached. On 18 March 2013 11:20, Tudor Popescu tud...@gmail.com mailto:tud...@gmail.com wrote: Hi Andreas I don't think it's about the OS (I'm on WInXP SP3, 32 bit, hosting Linux using Vritualbox), but about the environment variables, even though from what I could see, I had them all correctly set. I gave up and am just running this through FSL.. Tudor On 18 March 2013 11:13, Andreas Berger n0642...@students.meduniwien.ac.at mailto:n0642...@students.meduniwien.ac.at wrote: On Friday, February 01, 2013 17:12:00 Tudor Popescu wrote: Hi Doug Strangely, the basic mri_concat command now worked, and so did the full one. I think I initially had a \ at the end of my command, just after the file name, which should not have been there; although having tried again with the backslash reinstated at the end, the command still worked. Also, the Analyze in the QDEC GUI now completes without error as well. It's quite frustrating that I still don't know why it hasn't been working all this time, especially since I didn't really do anything different now (that I was aware of!) and the files were located on the same partition (Virtualbox's shared folder). Anyhow, thanks again for your kind help! Tudor On 31 January 2013 20:36, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 01/31/2013 12:30 PM, Tudor Popescu wrote: Hi Doug, I'm not sure why that does not make sense, shouldn't the input of mri_concat be several to-be-concatenated files rather than a single file? Sorry, I did not mean to imply that the command line was wrong, rather that the behavior did not make sense -- it should print *something* to the terminal. It does make sense to have multiple files, but it will also work with a single file. I just suggested this to make things simpler. Anyway, after trying out the command with only one of the files from the tutorial, /mri_concat --debug /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.* *thickness.fwhm10.fsaverage.mgh --o /media/Dell/_FS/buckner_data/** subjects/qdec/y.mgh/ ..the same thing happens, namely it returns to the command prompt, with no message whatsoever. What could be wrong? As I mentioned, all those MGH files are at the expected path. Thanks again for your help! What happens if you type mri_concat with no options at all? Tudor On 20 December 2012 05:24, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto: gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: That does not make sense. Try using only one input file. Also, put --debug as the first option. doug On 12/19/12 8:32 AM, Tudor Popescu wrote: Hi Doug, So the full command is mri_concat /media/Dell/_FS/buckner_data/**subjects/140/surf/lh.** thickness.fwhm10.fsaverage.mgh
Re: [Freesurfer] More QDEC questions
On 03/28/2013 03:53 PM, Tudor Popescu wrote: I was wondering if anybody is able to help with (any one of) these questions? That would be really helpful, as I could not find an answer on the wiki. Many thanks in advance! On 26 March 2013 20:44, Tudor Popescu tud...@gmail.com mailto:tud...@gmail.com wrote: Hi everyone, My QDEC analysis ran into an error message that seems to be a classic (and, so far, it seems unsolved), from mri_concat, which I've described in a separate message, just sent. I have, however, more theoretical questions about QDEC, which I hope some kind soul will help me with: - why does QDEC only provide the volume of /subcortical/ structures under StatsDataImport/aseg.volume, when the automatic GM/WM segmentation is done for the entire brain, not just for subcortical regions? No reason in particular. You can add them into the qdec table. - how are the volume measurements provided in aseg.volume different from the ones done obtained with a VBM analysis? Does VBM give segmentation volumes? I thought it was voxel-wise exploratory. - why is /volume /the result of /segmentation /(aseg.volume) whereas /thickness /derives from /parcelation /(rh.aparc.thickness)? Is it not the case that both operations (segmentation+parcellation) are necessary to calculate volume as well as thickness? You can get volume from parcellations too (this is supplied in the ?h.apac.stats file). You can't get thickness from non-surface structures like amygdala. - how is a QDEC thickness analysis different from a regular AN(C)OVA in which you are interested in main and interaction effects of the IVs on the DV? I ask this because some of the questions that appear in QDEC's Analysis Results tab – e.g. is the correlation between (DV) and (IV) different from zero? – would not (I think) be directly answerable by an ANOVA Often times they are the same, depends on the contrast. I don't know what IV and DV are so I can't answer your specific question. - would the same type of ANOVA done by QDEC be doable by extracting the values of the DV for each subject (using e.g. /aseg.volume/) and then doing the ANOVA in e.g. SPSS? If so, when would you do one versus the other? Yes. QDEC is an exploratory voxel-based method so effects don't have to lie cleanly within an ROI boundary. - why is it that only continuous factors (e.g. age) can be taken in the analysis as nuisance factors, when discrete variables (e.g. gender) might also be irrelevant for a particular analysis and thus belong to the Nuisance Factor list? It is just a matter of convenience in making the contrasts. ie, it is easy to extend our contrast making code to add nuisance continuous variables doug Many thanks in advance!! Tudor ___ 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 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.
Re: [Freesurfer] aseg.mgz altered after auto-recon2?
nope, you wouldn't benefit any further I don't think On Thu, 28 Mar 2013, Joshua Lee wrote: Hey thanks, I haven't worried about multi threading typically since I just run more brains simultaneously. On my computer, I have sufficient 64 gigs RAM (64 gigs) and 24 CPU/cores (not sure which) to run 20 recon-all scripts simultaneously at full speed. Would I still benefit from the multi threading? I am a little confused about cores vs cpus I created a copy of the recon-all script that stops at calabel step, and am running that now. - Josh On Thu, Mar 28, 2013 at 12:58 PM, Natalie Han zh...@stanford.edu wrote: Hi, Josh, I think you can run the autorecon1, subcortseg and no segstats if you don't want the statistics file (aseg.stats). Also, use -openmp 8 can speed up quite a lot by multi-threading. For a regular T1 brain image, I can the running time to get aseg.mgz in about 4-5 hours. recon-all -i subject autorecon1 -subcortseg -nosegstats -openmp 8 cheers, Natalie On Thu, Mar 28, 2013 at 12:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Josh, yes, I think that's correct. Bruce On Thu, 28 Mar 2013, Joshua Lee wrote: In fact, couldn't I stop after calabel if all I want is the aseg.mgz? - Josh On Thu, Mar 28, 2013 at 11:18 AM, Joshua Lee jki...@ucdavis.edu wrote: Hi All, Am I right in reading the dev table that if I just want the aseg.mgz, (not the stats output), I only need to run auto-recon1 and auto-recon2? I need to run 250+ brains just to get the aseg volume, so if I can shave off 4-10 hours off each that would be huge. ___ 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] specifying random effects in LME (Linear Mixed Effects models)
Jorge, Thanks for the clarification. I will try an analysis using [1 2 3] with all of the subjects with a minimum of 4 repeats and compare the results using the same analysis on all subjects with a minimum of 3 repeats. This is worthwhile for us since we lose quite a few when excluding those subjects with only 3 repeats. Your response also brings up the interesting point of what we can expect when including subjects with a single measure (I think a new feature in your longitudinal analysis). I guess they would contribute to specifying group differences at the level of the intercept? --Francois From: jorge luis jbernal0...@yahoo.esmailto:jbernal0...@yahoo.es Reply-To: jorge luis jbernal0...@yahoo.esmailto:jbernal0...@yahoo.es Date: Wednesday, March 27, 2013 4:58 PM To: Francois Lalonde flalo...@mail.nih.govmailto:flalo...@mail.nih.gov, freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models) Hi Francois If you want to test the model with three random effects including intercept, time, and time*time as the random effects then you should use [1 2 3] (these are the columns corresponding to those covariates in X). Actually, for the example in the wiki page we first tested [1 2 3] but the model [1 2] was the best at most vertices. In general, you need more than 4 repeated measures to think of including three random effects in the model for the covariance. Otherwise two random effects are usually enough (you can still include time*time in the model for the mean as in the wiki ). Also, computation time increases quickly with the number of random effects. There is an oncoming paper that will expand more on our longitudinal mass-univariate analyses with lme (hopefully soon). Best -Jorge De: Lalonde, Francois (NIH/NIMH) [E] flalo...@mail.nih.govmailto:flalo...@mail.nih.gov Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 27 de marzo de 2013 15:20 Asunto: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models) I am following the wiki page for LME analysis and I have a quick question. The Mass-univariate example near the bottom of the page proposes an initial model that contains intercept, linear and quadratic terms as random effects. However, the examples just below for lme_mass_fit_EM_init(), lme_mass_fit_EM_Rgw() only have [1 2] as selected random effects. Should the vector Zcols contain [1 2 3] as selected random effects in order to test the proposed model? Thanks, Francois François Lalonde, Ph.D. Child Psychiatry Branch NIMH / NIH 10 Center Drive, Room 3N202 Bethesda, MD 20892 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] specifying random effects in LME (Linear Mixed Effects models)
Hi Francois I think that you missunderstood a point of my previous answer. You should always include ALL subjects (those with 1,2,3,4... and so on repeated measures) in your analysis whether or not the model for the covariance includes one, two, three or more random effects. What I wanted to say in my previous answer is that you should have several subjects with more than four longitudinal measurements in your data set to start thinking of using such a complicated random effects covariance matrix as the one determined by an lme model including three random effects. Yes, subjects with a single measure contribute to more efficient and unbiased estimation of the between-subject variability. Best -Jorge De: Lalonde, Francois (NIH/NIMH) [E] flalo...@mail.nih.gov Para: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Enviado: Jueves 28 de marzo de 2013 16:45 Asunto: Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models) Jorge, Thanks for the clarification. I will try an analysis using [1 2 3] with all of the subjects with a minimum of 4 repeats and compare the results using the same analysis on all subjects with a minimum of 3 repeats. This is worthwhile for us since we lose quite a few when excluding those subjects with only 3 repeats. Your response also brings up the interesting point of what we can expect when including subjects with a single measure (I think a new feature in your longitudinal analysis). I guess they would contribute to specifying group differences at the level of the intercept? --Francois From: jorge luis jbernal0...@yahoo.esmailto:jbernal0...@yahoo.es Reply-To: jorge luis jbernal0...@yahoo.esmailto:jbernal0...@yahoo.es Date: Wednesday, March 27, 2013 4:58 PM To: Francois Lalonde flalo...@mail.nih.govmailto:flalo...@mail.nih.gov, freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models) Hi Francois If you want to test the model with three random effects including intercept, time, and time*time as the random effects then you should use [1 2 3] (these are the columns corresponding to those covariates in X). Actually, for the example in the wiki page we first tested [1 2 3] but the model [1 2] was the best at most vertices. In general, you need more than 4 repeated measures to think of including three random effects in the model for the covariance. Otherwise two random effects are usually enough (you can still include time*time in the model for the mean as in the wiki ). Also, computation time increases quickly with the number of random effects. There is an oncoming paper that will expand more on our longitudinal mass-univariate analyses with lme (hopefully soon). Best -Jorge De: Lalonde, Francois (NIH/NIMH) [E] flalo...@mail.nih.govmailto:flalo...@mail.nih.gov Para: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Enviado: Miércoles 27 de marzo de 2013 15:20 Asunto: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models) I am following the wiki page for LME analysis and I have a quick question. The Mass-univariate example near the bottom of the page proposes an initial model that contains intercept, linear and quadratic terms as random effects. However, the examples just below for lme_mass_fit_EM_init(), lme_mass_fit_EM_Rgw() only have [1 2] as selected random effects. Should the vector Zcols contain [1 2 3] as selected random effects in order to test the proposed model? Thanks, Francois François Lalonde, Ph.D. Child Psychiatry Branch NIMH / NIH 10 Center Drive, Room 3N202 Bethesda, MD 20892 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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
Re: [Freesurfer] bbr problem run
Here are the errors from the trac-all.log file I sent earlier: mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/Test_FS/mri/ERROR: /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/Test_FS/mri/ERROR: /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister.nii ** ERROR (nifti_image_read): failed to find header file for '/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ERROR: Could not open image /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ** ERROR (nifti_image_read): failed to find header file for '/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ERROR: Could not open image /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ERROR: cannot open /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/reg.init.dat.fsl.mat ERROR: reading /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/anatorig2diff.bbr.dat Image Exception : #22 :: ERROR: Could not open image /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/diff/White-Matter++.flt ERROR: Could not open /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/mni2diff.bbr.mat ERROR: Could not read /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz ERROR: Could not read /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz On Thu, Mar 28, 2013 at 4:22 PM, Salil Soman salso...@stanford.edu wrote: Thank you for your response. I tried re-running Tracula using bbr in a subject I had successfully run using flt. trac-all prep and bedp worked without an error. Bedpostx sent me an email confirming bedpost completed without problem. However, when I try to run trac-all paths, I get the following error: Loading atlas reference volume from /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.$ niiRead(): error opening file /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz ERROR: Could not read /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz recon-all did finish without error. Best wishes, -S On Thu, Mar 28, 2013 at 8:43 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sal, 1. I have no experience with the sun grid engine, perhaps someone else on the list can help with that. 2. The -bedp step needs the outputs from the -corr and -masks steps. The -path step needs the outputs from the -bedp step. The output files from each part are listed here: http://www.freesurfer.net/**fswiki/trac-all#** Outputdirectoriesandfileshttp://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles 3. Checking the aparc+aseg should be enough for tracula purposes as well, since that's the freesurfer output that tracula uses. Keep in mind that DWI resolution is usually lower than T1 resolution, so tiny changes in the aparc+aseg might not affect tracula at all. 4. Yes, I do recommend using bbregister. It's not surprising that it would give better results since it uses the additional information of the surfaces. If I remember correctly, Doug didn't manage to replicate your bbregister error, right? I'd check if you get the same error with the 5.1 version of bbregister. Hope this helps, a.y On Wed, 27 Mar 2013, Salil Soman wrote: Hi, I have been able to implement FS 5.2 on our Sun Grid Engine Cluster using the CentOS 6 distribution. After modifying the fsl_sub_mgh file to work with out cluster queue names and to modify the email notifications, I am able to run the entire processing pipeline using FLT. (Everytime I try bbr I get errors. I had email doug about this but have not heard any response). I am submitting the jobs to the cluster as follows recon-all -i ./*.nii -s WCA_0202_T1_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all trac-all -prep -no-isrunning -c
Re: [Freesurfer] Correlation with cortical thickness
It was brought to my attention that the previous link was broken. Here is a corrected link: http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2656.2002.00618.x/abstract The paper reference is: On the misuse of residuals in ecology: regression of residuals vs. multiple regression 1. Robert P. Freckleton* Article first published online: 8 MAY 2002 DOI: 10.1046/j.1365-2656.2002.00618.x Issue [image: Journal of Animal Ecology] Journal of Animal Ecology Volume 71, Issue 3, http://onlinelibrary.wiley.com/doi/10./jae.2002.71.issue-3/issuetocpages 542–545, May 2002 Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Wed, Mar 27, 2013 at 3:46 PM, MCLAREN, Donald mclaren.don...@gmail.comwrote: Here is a link describing the difference in the methods: http://onlinelibrary.wiley.com/store/10.1046/j.1365-2656.2002.00618.x/asset/j.1365-2656.2002.00618.x.pdf?v=1t=heswinwbs=dce1a222e16e861d105340fd919c65fb43dc39ac Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Wed, Mar 27, 2013 at 3:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: In the 2nd option, age and weight (and other variables) are simultaneously fit to the data. Most people refer to this as regressing out the effect of one variable when looking at the other. But it is not regressing out age and then looking at the correlation of age with the residual. doug On 03/27/2013 07:02 AM, Martijn Steenwijk wrote: Dear all, I've a question regarding computing correlations with cortical thicknesses on the surface; Suppose I have two variables for each subject: (age and weight) and I want to compute the correlation between cortical thickness and weight, corrected for age. Option 1: Fsgd contains: Variables weight Contrast file contains: 0 1 Option 2: Fsgd contains: Variables age weight Contrast file contains: 0 0 1 Is it true that the effect of age is regressed out in the second option; and it computes the correlation between CT and weight after correcting for age? Best, Martijn ___ 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 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
[Freesurfer] coregistering- ideal CT type
Hi freesurfers, I working on a coregistration right now with a few different CT scans. None of them have looked that good with tkregister (for example when I used one CT scan, the electrodes didn't even show up). Is there an certain CT I need to be using? Thanks, m ___ 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] Linear Mixed modal
Contrast creation is the same in all programs. It is based on the design matrix. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Mon, Mar 25, 2013 at 11:50 PM, xiangbo_2010 xiangbo_2...@126.com wrote: Dear experts Whether can the design of contrast in freesurfer 5.2 the same as SPM? it is difficult to make the contrast in freesurfer if the categorical variables were much more, specifically compute the interaction or F-test in study. Thanks！ Bo Xiang ___ 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] contrast matrix
On Wed, Mar 27, 2013 at 2:53 AM, xiangbo_2010 xiangbo_2...@126.com wrote:
Dear Prof Donald McLaren
I am sorry to disturb you! I have four discrete variables {factor 1(A,B),
factor 2(C,D), factor 3(G,H), and gender(M,F)} and a continuous variable
(age), I want to use the GLM to analysis the result of the interaction
among factor 1(A,B), factor 2(C,D) and factor 3(E,F)
regressing out the effect of gender and age, and I have 16 classes:
MACG,MACH, MADG, MADH, MBCG, MBCH, MBDG, MBDH, FACG,FACH, FADG, FADH,
FBCG, FBCH, FBDG, FBDH, so I design the contrast is following:
1 -1 -1 1 -1 1 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 1 -1 -1 1 -1 1 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
IF - and this is a big if -- the columns are as you have described in this
order, then the contrast should be:
1 -1 -1 1 -1 1 1 -1 1 -1 -1 1 -1 1 1 -1
To create any contrast, you need to start with the null hypothesis and then
you can build up the contrast from its smaller elements:
This is for a design with 18 subjects in group 1, 9 subjects in group
2, 2 group terms and 7 conditions: Start with the simpliest element,
single subject in a single condition, build its contrast, repeat for
all subjects and conditions, and then combine the ones you want.
S1G1C1=[1 zeros(1,26) 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0]
S1G1C2=[1 zeros(1,26) 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0]
Now average your G1C1 and by summing and dividing by the number of
subjects, you'd get
G1C1=[ones(1,18)/18 zeros(1,9) 1 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
0]
and
G1C2=[ones(1,18)/18 zeros(1,9) 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
0]
and
G2C1=[zeros(1,18) ones(1,9)/9 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0]
and
G2C2=[zeros(1,18) ones(1,9)/9 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0]
Now subtract G1C1-G1C2 AND G2C2-G2C1
G1C1-G1C2=[zeros(1,27) 0 0 1 -1 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0]
and
G2C1-G2C2=[zeros(1,27) 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0]
Now subtract these two:
Interaction contrast=[zeros(1,27) 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 -1
1 0 0 0 0 0]
In your case, if you start with G-H for Males in group A/C:
1 -1 0 0 0 0...
Then Males in group A/D:
0 0 1 -1 0 0
Subtracting these gives you the interaction of factor 2 and 3 for A males.
1 -1 -1 1 0 0 0 0 0...
You can repeat for A females.
0 0 0 0 0 0 0 0 1 -1 -1 1 0 0 0 0
Now you can do the same for B males and B females:
0 0 0 0 1 -1 -1 1 0 0 0 0 0 0 0 0 and 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 -1 1
Now subtract A from B after adding males and females:
1 -1 -1 1 -1 1 1 -1 1 -1 -1 1 -1 1 1 -1
This will work for any contrast that you ever want to make.
is correct? thank you very much!
look forward for your reply!
Bo Xiang
At 2012-11-21 04:07:37,MCLAREN, Donald mclaren.don...@gmail.com
wrote:
On Tue, Nov 20, 2012 at 12:56 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Thanks Donald. Is this the standard way to do this? I had used 8 rows
instead of 4 with the difference being that 8 rows gives you an opportunity
to look for an effect in males OR females.
Yes. Having 8 rows would tell you if you have an interaction between
factor 1 and 2 in either males or females. My 4 rows only tell you if
the interaction exists. Technically speaking, one would run the
three-way interaction first. If nothing existed then you do the
two-way interaction as I suggested. If there is a three-way
interaction, then you would use Doug's approach of the interaction in
either males or females.
If there is an effect in both
males and females but the effects go in opposite directions, then the 4 row
implementation will resolve to 0 (no effect). Or am I misunderstanding
something (again:)?
Nope. You are right. If the male and female effects are different,
then they could cancel each other out. If you suspect this to be the
case, then you should be able to demonstrate a three-way interaction.
thanks!
doug
On 11/20/2012 01:50 PM, MCLAREN, Donald wrote:
Bo,
Doug asked me to chime in on your issue. Here are some points that you
(and others) will hopefully find useful.
(1) Inferences are two-step process. First, you create and estimate
the design matrix. Every column in the design matrix accounts can
account for some of the variance in the data. Second, you have
contrasts that allow you to infer specific effects. Because the model
contains your covariates, you are always controlling for the
covariates and by extension any factor/covariate not in the contrast.
(2) Forming contrasts is often the most difficult thing to do. I
assume that your three factors (1, 2, and gender) are all
between-subject factors. If one of them is a within-subject factor
please let me know and disregard the rest of the email. The final
F-contrast will have 4 rows (factor 1 levels-1)*(factor 2 levels
-1)=(3-1)*(3-1)=2*2=4
The following is an outline for creating
[Freesurfer] odd tkregister
Hi freesurfers, In using tkregister, I generated an odd (see attached): the image not only looks sheered but there is an old white box showing up. I'm not sure how to resolve this. Thanks a lot, Mia attachment: freesurfer.PNG___ 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] FS version of Colin27
Hi FS experts: I am trying to map AAL template onto FS surface to create surface-based AAL template. Several days ago, i asked this question, and Garikoitz Lerma gave me some suggestions. Possibly, i think the process is like as folllows: 1. downloa the Colin27 subject in Surfrend page, and transform it to the latest FS version (5.2 currently). 2. obtain register.dat between Colin27 subject and single_subj_T1.nii under the canonical directory in SPM8 using bbregister. bbregister --s Colin27_subject --mov single_subj_T1.nii --reg register.dat --init-fsl --t1 3. transfrom each AAL ROI to the surface file with register.dat file obtained above using mri_vol2surf. mri_vol2surf --mov AAL_ROI.nii --reg register.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh \ --out lh.Colin27_AALROI.mgh --reshape 4. use mri_label2label or mri_segstat to obtain the cortical thickness of each ROI for individual subject. My question is about the first step. How to transform the Colin27 subject to FS version 5.2? that is to say how can i get the FS version of Colin27 template instead of fsaverage template? Hope someone gives me some suggetions. Besh wishes. ___ 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.
