[Freesurfer] fitting a priori ROI masks to freesurfer
Dear all, I have an a priori ROI mask previously created in AFNI for functional data. My hypothesis requires me to derive cortical thickness values for the same ROIs. How would I obtain the values using these ROIs from freesurfer? The mask was generated in Talairach space and are surface level ROIs. I tried using mris_anatomical_stats but it didn't seem to work (possibly because the masks weren't created using freesurfer/weren't saved in .label files). How would I proceed? I realize this is probably pretty simple but I'm new to freesurfer and really appreciate any guidance. -- Sonya Kaur Clinical Psychology Graduate Student Department of Psychology The University of Texas, Austin 1 University Station, A8000 Austin, TX 78712 SEA 4.110E sonya_k...@mail.utexas.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] make_average_subject
Hi Sonya did you run out of RAM? How much is on your machine? cheers Bruce On Fri, 23 Mar 2012, sonya kaur wrote: > Dear all,I'm getting an error with the make_average_subject command on > freesurfer. The error is vm_allocate (size=262144) failed (error code 3). > According to the freesurfer helpdesk, it seems to be a problem with creating > an "average" aseg. Is there any solution for this that you know of? > > Thank you in advance! > > -- > Sonya Kaur > Clinical Psychology Graduate Student > Department of Psychology > The University of Texas, Austin > 1 University Station, A8000 > Austin, TX 78712 > SEA 4.110E > sonya_k...@mail.utexas.edu > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] make_average_subject
Dear all, I'm getting an error with the make_average_subject command on freesurfer. The error is vm_allocate (size=262144) failed (error code 3). According to the freesurfer helpdesk, it seems to be a problem with creating an "average" aseg. Is there any solution for this that you know of? Thank you in advance! -- Sonya Kaur Clinical Psychology Graduate Student Department of Psychology The University of Texas, Austin 1 University Station, A8000 Austin, TX 78712 SEA 4.110E sonya_k...@mail.utexas.edu ___ 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] Fwd: Skull strip failure
Hi, I've uploaded my subject to the FTP server. The file is called AL.zip. I'm really enjoying using freesurfer and I'm excited to hear what you think about this subject. Thanks so much for the help. -- Vincent On Thursday, March 22, 2012 at 8:25 AM, Louis Nicholas Vinke wrote: Hi Vincent, Yep, that'll work or the web file drop, whichever you prefer. https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html -Louis On Thu, 22 Mar 2012, Vincent wrote: Hi Louis, Thank you very much! I'm eager to upload something but I am stuck working another job until later today. I'll have to wait until then because I've never uploaded something to your servers and I'll have to figure out the best way to go about it. I believe I should upload to ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Thanks again. -- Vincent On Thursday, March 22, 2012 at 7:42 AM, Louis Nicholas Vinke wrote: Hi Vincent, Let me know when you upload this case, I think I may be able to help. -Louis On Wed, 21 Mar 2012, Vincent wrote: Hi, I have an image that is completing the skull strip with a lot of skull remaining and it is have a large effect on the surfaces. I've tried lowering the watershed threshold as low as 5 and I've tried adding the -gcut option, but the low threshold by itself does not eliminate the skull and gcut not only fails to remove the skull but it removes cerebellum as well. There is so much skull left that I am hesitant to try manual edits, but I don't know any other options. Are there any? By the way, this brain is from an older individual with pretty substantial atrophy. --Vincent 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] trac-all -path error
Yes. On Fri, 23 Mar 2012, Chris Watson wrote: > Ok. Do I run it with the defaults? > # fibers per voxel = 2 > ARD weight = 1 > burn-in period = 1000 > # jumps = 1250 > sample every = 25 > > On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: >> >> Oh, ok. That's a known issue, it has to do with changes in the command >> line of the latest version of bedpostx. We've updated trac-all and it'll >> be working in our next release but for now you'll have to run bedpostx by >> itself and not through trac-all. Sorry for the inconvenience! >> >> On Fri, 23 Mar 2012, Chris Watson wrote: >> >> > [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ >> > dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz >> > mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz >> > th1samples.nii.gz >> > >> > >> > Come to think of it, when I ran bedpostx, it only output "1 slice >> > processed", but repeated 70 times, or however many slices there are. The >> > data is from a Siemens 3T, by the way. >> > >> > On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >> > > >> > > What's in the diff_slices directory? That's a temporary directory >> > > that >> > > bedpostx creates and that gets deleted after the results get >> > > "merged". So >> > > my guess would be that bedpostx didn't finish processing. >> > > >> > > On Fri, 23 Mar 2012, Chris Watson wrote: >> > > >> > > > Hello, I successfully ran trac-all -bedp, and when I run the next >> > > step I >> > > > get the following error: >> > > > > Loading BEDPOST parameter samples from >> > > > >> > > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >> > > > niiRead(): error opening file >> > > > >> > > >> > > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > > >> > > > > ERROR: Could not read >> > > > >> > > >> > > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > > >> > > > > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed >> > > Mar 7 >> > > > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> > > > > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >> > > > > Word too long. >> > > > >> > > >> > > >> > > >> > > > > Indeed, the "merged" file doesn't exist. I am running >> > > Freesurfer 5.1.0 >> > > > and FSL 4.1.9. >> > > > Here's what's in the dmri.bedpostX directory: >> > > > > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >> > > > bvals bvecs commands.txt diff_slices logs monitor >> > > > nodif_brain_mask.nii.gz xfms >> > > > > ___ >> > > > 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] trac-all -path error
Ok. Do I run it with the defaults? # fibers per voxel = 2 ARD weight = 1 burn-in period = 1000 # jumps = 1250 sample every = 25 On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: > > Oh, ok. That's a known issue, it has to do with changes in the command > line of the latest version of bedpostx. We've updated trac-all and > it'll be working in our next release but for now you'll have to run > bedpostx by itself and not through trac-all. Sorry for the inconvenience! > > On Fri, 23 Mar 2012, Chris Watson wrote: > >> [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ >> dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz >> mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz >> th1samples.nii.gz >> >> >> Come to think of it, when I ran bedpostx, it only output "1 slice >> processed", but repeated 70 times, or however many slices there are. >> The data is from a Siemens 3T, by the way. >> >> On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >>> >>> What's in the diff_slices directory? That's a temporary directory that >>> bedpostx creates and that gets deleted after the results get >>> "merged". So >>> my guess would be that bedpostx didn't finish processing. >>> >>> On Fri, 23 Mar 2012, Chris Watson wrote: >>> >>> > Hello, I successfully ran trac-all -bedp, and when I run the next >>> step I >>> > get the following error: >>> > > Loading BEDPOST parameter samples from >>> > >>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >>> > niiRead(): error opening file >>> > >>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >>> >>> > > ERROR: Could not read >>> > >>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >>> >>> > > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed >>> Mar 7 >>> > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >>> > > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >>> > > Word too long. >>> > >>> >>> >>> > > Indeed, the "merged" file doesn't exist. I am running >>> Freesurfer 5.1.0 >>> > and FSL 4.1.9. >>> > Here's what's in the dmri.bedpostX directory: >>> > > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >>> > bvals bvecs commands.txt diff_slices logs monitor >>> > nodif_brain_mask.nii.gz xfms >>> > > ___ >>> > 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] trac-all -path error
Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience! On Fri, 23 Mar 2012, Chris Watson wrote: > [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ > dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz > mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz > th1samples.nii.gz > > > Come to think of it, when I ran bedpostx, it only output "1 slice processed", > but repeated 70 times, or however many slices there are. The data is from a > Siemens 3T, by the way. > > On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >> >> What's in the diff_slices directory? That's a temporary directory that >> bedpostx creates and that gets deleted after the results get "merged". So >> my guess would be that bedpostx didn't finish processing. >> >> On Fri, 23 Mar 2012, Chris Watson wrote: >> >> > Hello, I successfully ran trac-all -bedp, and when I run the next step I >> > get the following error: >> > >> > Loading BEDPOST parameter samples from >> > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >> > niiRead(): error opening file >> > >> > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > >> > >> > ERROR: Could not read >> > >> > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > >> > >> > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 >> > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> > >> > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >> > >> > Word too long. >> > >> > >> > Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 >> > and FSL 4.1.9. >> > Here's what's in the dmri.bedpostX directory: >> > >> > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >> > bvals bvecs commands.txt diff_slices logs monitor >> > nodif_brain_mask.nii.gz xfms >> > >> > ___ >> > 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] trac-all -path error
[freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz th1samples.nii.gz Come to think of it, when I ran bedpostx, it only output "1 slice processed", but repeated 70 times, or however many slices there are. The data is from a Siemens 3T, by the way. On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: > > What's in the diff_slices directory? That's a temporary directory that > bedpostx creates and that gets deleted after the results get "merged". > So my guess would be that bedpostx didn't finish processing. > > On Fri, 23 Mar 2012, Chris Watson wrote: > >> Hello, I successfully ran trac-all -bedp, and when I run the next step I >> get the following error: >> >> Loading BEDPOST parameter samples from >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >> niiRead(): error opening file >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> >> >> ERROR: Could not read >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> >> >> Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 >> 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> >> trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >> >> Word too long. >> >> >> Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 >> and FSL 4.1.9. >> Here's what's in the dmri.bedpostX directory: >> >> [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >> bvals bvecs commands.txt diff_slices logs monitor >> nodif_brain_mask.nii.gz xfms >> >> ___ >> 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] trac-all -path error
What's in the diff_slices directory? That's a temporary directory that bedpostx creates and that gets deleted after the results get "merged". So my guess would be that bedpostx didn't finish processing. On Fri, 23 Mar 2012, Chris Watson wrote: > Hello, I successfully ran trac-all -bedp, and when I run the next step I > get the following error: > > Loading BEDPOST parameter samples from > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX > niiRead(): error opening file > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz > ERROR: Could not read > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux > > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 > > Word too long. > > > Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 > and FSL 4.1.9. > Here's what's in the dmri.bedpostX directory: > > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ > bvals bvecs commands.txt diff_slices logs monitor > nodif_brain_mask.nii.gz xfms > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] trac-all -path error
Hello, I successfully ran trac-all -bedp, and when I run the next step I get the following error: Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 Word too long. Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 and FSL 4.1.9. Here's what's in the dmri.bedpostX directory: [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ bvals bvecs commands.txt diff_slices logs monitor nodif_brain_mask.nii.gz xfms ___ 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] Cutting closed line for flat map
Hi Bruce, I tried opening a new tksurfer and not clicking in it except to cut this circle. Specifically, I opened the inflated surface, loaded the curvature and previously saved patch, then drew the circle (having not clicked in the window at all), finally clicking cut closed line. I still get the extra line tangential to the cut circle. I also tried opening a different subject (without a previously saved patch), drawing the anterior relaxation line, then drawing an intersecting circle and hitting cut closed line. Again, I get the additional line tangential to the circle. There does appear to be a GUI bug with respect to de-selecting cut points. If I click 5 different vertices, and then right-click, the first four go away but the fifth appears to stay. However, if I then click elsewhere the fifth point goes away and a new sixth point appears. The sixth point can be option-clicked to make it disappear, so that no cut points remain highlighted. Importantly, the tangential line has nothing to do with these six cut points (in occipital cortex, but the line still goes toward orbitofrontal PFC). --Greg Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burge...@pcg.wustl.edu On Mar 23, 2012, at 9:51 AM, Bruce Fischl wrote: > Hi Greg > > do you see this on all your datasets? I don't think I've seen this unless > it's because one forgets to right click before starting > > Bruce > On Fri, 23 Mar 2012, Greg Burgess wrote: > >> Hi Bruce, >> >> I've been using the "Unmark Vertices" option from the edit menu, but I've >> also tried right-clicking the image and it doesn't make a difference. >> >> I've also tried clicking things in order, deleting cut points that might be >> out of order. >> >> I've been trying to understand the issue by starting with very small >> circles, then expanding them in size or changing their location. It seems >> that there are certain portions of the medial wall that can't be included in >> the cut without things going awry. I'm attaching a couple of snapshots to >> show an example. I've tried numerous times to cut a small circle in this >> region, and always end up with an additional line running ventrally from the >> existing cut line. >> > > > 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] recon-all error
Hi Sue what is the final error? The last few lines of the recon-all.log? This message occurs sometimes and doesn't really matter. cheers Bruce On Fri, 23 Mar 2012, Susan Ruiz wrote: Hello all, I have been using FS5.0 and just started using 5.1. I tried running a recon with the new version with two of my subjects, and in both cases I got the same error message: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUN CTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 7003.6 tol 0.10 This error did not stop the rest of the recon from running for quite some time after the error, however, it ultimately exited with errors. I searched the mail archive and found reference to this error message, but I couldn't identify how it was resolved/what the cause of it might be. Any suggestions as to what might be causing this? Thanks, ~Sue * * ** *** * * Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smos...@bu.edu * * ** *** * * ___ 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] Cutting closed line for flat map
Hi Greg do you see this on all your datasets? I don't think I've seen this unless it's because one forgets to right click before starting Bruce On Fri, 23 Mar 2012, Greg Burgess wrote: > Hi Bruce, > > I've been using the "Unmark Vertices" option from the edit menu, but I've > also tried right-clicking the image and it doesn't make a difference. > > I've also tried clicking things in order, deleting cut points that might be > out of order. > > I've been trying to understand the issue by starting with very small circles, > then expanding them in size or changing their location. It seems that there > are certain portions of the medial wall that can't be included in the cut > without things going awry. I'm attaching a couple of snapshots to show an > example. I've tried numerous times to cut a small circle in this region, and > always end up with an additional line running ventrally from the existing cut > line. > ___ 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 error
Hello all, I have been using FS5.0 and just started using 5.1. I tried running a recon with the new version with two of my subjects, and in both cases I got the same error message: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUN CTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 7003.6 tol 0.10 This error did not stop the rest of the recon from running for quite some time after the error, however, it ultimately exited with errors. I searched the mail archive and found reference to this error message, but I couldn't identify how it was resolved/what the cause of it might be. Any suggestions as to what might be causing this? Thanks, ~Sue * * ** *** * * Susan M. M. Ruiz, Ph.D. Boston University School of Medicine Laboratory for Neuropsychology VA Boston Healthcare System smos...@bu.edu * * ** *** * * ___ 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] mkbrainmask-sess
Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). Any help with this would be much appreciated. Thanks Kiley FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHSfslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # -- Using FSL's BET to Extract Brain-- # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdlinemri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostnameFreeSurfer machine i686 user virtualuser input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0 ___ 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] Cutting closed line for flat map
Hi Greg two possible problem: 1. Make sure you right click before starting to define medial wall so all other clicks are erased. 2. Make sure you click in the order you want things connected. cheers Bruce On Fri, 23 Mar 2012, Greg Burgess wrote: > I'm trying to cut the medial wall as described in Step 2 on > http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch . > However, each time I click "Cut Closed Line", I get a jumble of lines that go > all over the cortex and medial wall, rather than a clean circle around the > medial wall. I've tried putting cut points so close that they're nearly on > top of each other, but it still doesn't help. > > Does anyone have an idea why this won't cut right? > > Thanks, > --Greg > > > Greg Burgess, Ph.D. > Staff Scientist, Human Connectome Project > Washington University School of Medicine > Department of Anatomy and Neurobiology > Email: burge...@pcg.wustl.edu > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Cutting closed line for flat map
I'm trying to cut the medial wall as described in Step 2 on http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch . However, each time I click "Cut Closed Line", I get a jumble of lines that go all over the cortex and medial wall, rather than a clean circle around the medial wall. I've tried putting cut points so close that they're nearly on top of each other, but it still doesn't help. Does anyone have an idea why this won't cut right? Thanks, --Greg Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Anatomy and Neurobiology Email: burge...@pcg.wustl.edu ___ 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] Checkout release and stable branch
Hi Nick,
the ./setup_configure works perfectly on the stable branch whereas it looks
like it is not working anymore on the dev branch.
With a checkout from last week I didn't have this issue.
(ubuntu 12.04 beta 1)
(libtool 2.4.2)
(automake 1.11.3)
*toor@linux:~/cvsroot/dev $>** ./setup_configure*
configure.in:3302: the top level
configure.in:3337: required file `gradient_nonlin_unwarp/Makefile.in' not
found
configure.in:3337: required file
`gradient_nonlin_unwarp/gradient_coil_files/Makefile.in' not found
Makefile.am:303: required directory ./gradient_nonlin_unwarp does not exist
autoreconf: automake failed with exit status: 1
*
toor@linux:~/cvsroot/dev $>*
I could remove this directory from the configuration/dependencies but I'm
not sure this is a good fix.
Do you experience the same behavior as well?
Thanks,
Nicolas
On Thu, Mar 22, 2012 at 3:18 PM, Nicolas Rannou wrote:
> Thanks for the quick answer :)
>
> I'm not very familiar with cvs and was assuming 'stable' was only the name
> of the directory in which the code would be checked out!
>
> Thanks!
> Nicolas
>
>
> On Thu, Mar 22, 2012 at 3:09 PM, Nick Schmansky > wrote:
>
>> the last arg should be 'dev', not 'stable'.
>> > Hi all,
>> >
>> > I followed the instructions on the wiki but it seems impossible to
>> > checkout
>> > the stable and release branches?
>> >
>> > [toor@linux:x86_64-Linux]...or/cvsroot/test$>cvs -d
>> > :pserver:anonym...@fsvm.nmr.mgh.harvard.edu:/usr/fscvsroot checkout -P
>> -r
>> > stable5 stable
>> > cvs server: cannot find module `stable' - ignored
>> > cvs [checkout aborted]: cannot expand modules
>> >
>> >
>> > Did their name changed?
>> >
>> > Is there a good way with cvs to list the available branches?
>> > ('cvs ls' not woking)
>> >
>> > Thanks,
>> > Nicolas
>> > ___
>> > 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.
>>
>>
>
___
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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
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Re: [Freesurfer] Cortical Normalization Questions
Our reply to that is here http://bjp.rcpsych.org/content/196/5/414.2.long which reminded me of other papers that have also used a global thickness measure to covary for mean cortical thickness and thereby "address whether any regional thickness differences were in excess of global cortical thickness differences between groups" -- see references [1,4] in our Reply. cheers, -MH > Hi Michael and others, > > maybe it's this one: > > http://bjp.rcpsych.org/content/196/5/414.1.long > > best, > -joost > > > On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms > wrote: > >> >> Hi Jeff, >> I personally like the idea of using average thickness as a covariate to >> control for a reduction in "whole brain" thickness, and have used that >> approach in a paper. If the Abstract that you mentioned indicated that >> this is flawed, I'd be curious to know what the reason was... >> >> cheers, >> -MH >> >> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: >> > Hi Jeff >> > >> > yes, I think this is still our recommendation for thickness, although >> > perhaps David Salat can verify. As far as surface area, you might get >> > Anderson Winkler to send you a preprint of his newly accepted paper on >> > surface area comparisons and how to do them properly. I would have >> said >> > normalize by the 2/3 root of ICV (maybe David can comment on this as >> well) >> > >> > cheers >> > Bruce >> > >> > >> > On Thu, 22 Mar 2012, Jeff Sadino wrote: >> > >> > > Hello, >> > > For cortical thickness normalizations, Bruce said not to normalize >> based on a HBM >> > > abstract >> > > ( >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). >> Is >> > > this still the consensus? >> > > >> > > For cortical volume, it is pretty standard to normalize to eTIV. >> > > >> > > For cortical surface area (jacobian), I couldn't find any >> information >> on the wiki. >> > > Does anyone have any recommendations? >> > > >> > > Thank you, >> > > Jeff >> > > >> > > >> > ___ 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical Normalization Questions
Hi Michael and others, maybe it's this one: http://bjp.rcpsych.org/content/196/5/414.1.long best, -joost On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms wrote: > > Hi Jeff, > I personally like the idea of using average thickness as a covariate to > control for a reduction in "whole brain" thickness, and have used that > approach in a paper. If the Abstract that you mentioned indicated that > this is flawed, I'd be curious to know what the reason was... > > cheers, > -MH > > On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: > > Hi Jeff > > > > yes, I think this is still our recommendation for thickness, although > > perhaps David Salat can verify. As far as surface area, you might get > > Anderson Winkler to send you a preprint of his newly accepted paper on > > surface area comparisons and how to do them properly. I would have said > > normalize by the 2/3 root of ICV (maybe David can comment on this as > well) > > > > cheers > > Bruce > > > > > > On Thu, 22 Mar 2012, Jeff Sadino wrote: > > > > > Hello, > > > For cortical thickness normalizations, Bruce said not to normalize > based on a HBM > > > abstract > > > ( > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html). > Is > > > this still the consensus? > > > > > > For cortical volume, it is pretty standard to normalize to eTIV. > > > > > > For cortical surface area (jacobian), I couldn't find any information > on the wiki. > > > Does anyone have any recommendations? > > > > > > Thank you, > > > Jeff > > > > > > > > ___ 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 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.
