Re: [Freesurfer] too much white matter
Hi Bruce, it worked! The surfaces now look so much better. Thanks for your help! Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 17:18:26 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, yes, it is an mp2rage image. I'm gonna work in your suggestions and see if it changes anything after rerunning the the recon-all process. Thank you! Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 16:18:06 Betreff: Re: [Freesurfer] too much white matter Hi Clara the second control point (135, 152, 163) is outside the brainmask. You will need to correct the skull stripping first. In general I wouldn't put control points in that type of location as it is certainly partial volumed. I would try something like 139, 145, 163 instead (and maybe a couple around there). Also, I assume the skull stripping failed as this is not the typical type of image we expect (since the background is so bright and noisy). Is it an mp2rage or something? There appears to be very little space between skull and brain so the stripping may be challenging, particularly in the orbitofrontal region where you had this control point (it looks like fat is shifting upwards either into or adjacent to brain) cheers Bruce On Tue, 30 Jun 2015, Clara Kühn wrote: oh, and here are the Freesurfer coordinates for the control points: 86, 143, 147 135, 152, 163 Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 11:39:40 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, thanks for your reply. As far as I can tell the cps are in the WM. I'd be grateful if you could take a closer look, though. You can download the dataset here: https://bigmail.cbs.mpg.de/i/2581030103b072173ff426e67d298cf4.zip Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 29. Juni 2015 18:07:28 Betreff: Re: [Freesurfer] too much white matter Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ 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 ___ 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] correction for field dishomogeneity
Hi Clelia, I think the reviewer might refer to the -3T flag of recon-all which enables 3T-specific NU intensity correction parameters and usage of a special atlas for Talairach alignment. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von clelia pellicano Gesendet: Freitag, 3. Juli 2015 18:55 An: Freesurfer support list Betreff: Re: [Freesurfer] correction for field dishomogeneity I did it. Thank you very much. C Il giorno 03/lug/2015 18:51, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu ha scritto: not sure. Did you use recon-all? If so, then you did use the appropriate pipeline provided by freesurfer On Fri, 3 Jul 2015, clelia pellicano wrote: Hi Bruce, thank you for your reply. Do you have any idea about what they could mean saying without using the appropriate pipeline provided by freesurfer? Thanks BW C Il giorno 03/lug/2015 15:32, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu ha scritto: Hi Clelia yes, we correct for field inhomogeneity. Presumably they mean the B1 receive field, which is what is typically meant in structurals. If they mean B0, we don't typically correct (nor do most people for structural imaging - this is more of an issue for diffusion and functional MRI). cheers Bruce On Fri, 3 Jul 2015, clelia pellicano wrote: Dear experts, I was wondering how freesurfer corrects for field dishomogeneity. As long as I know, it's automatically done by the software . My concern is because a reviewer has made this comment (please find it below): Authors used an old 3 T MRI without using the appropriate pipeline provided by freesurfer to correct for field dysomogeneity We have run the standard pipeline provided to derive measures of cortical thickness and deep grey matter nuclei volume (FreeSurfer version 5.3.0 ). Here the MRI protocol used: All participants were scanned on a 3-Tesla Philips Intera whole-body MRI scanner. A T1-weighted three-dimensional magnetization-prepared rapid acquisition gradient-echo (MPRAGE; time echo: 4.6 ms; time repetition: 9.7ms; field of view: 240 ms; voxel size= 1 x1 x 1 mm) was acquired. Any clue about? Thank you in advance. BW Clelia . Clelia Pellicano, MDPhD Student in Clinical and Experimental Neurosciences and Psychiatry, Department of Neuroscience, Mental Health and Sensory Organs, NESMOS, Sapienza University Via di Grottarossa 1035, 00189 Rome, Italy phone +390633775579 fax +390633775900 Research Neurologist Department of Clinical and Experimental Neurology Santa Lucia Foundation IRCSS Via Ardeatina 306, 00179, Rome, Italy ___ 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.edumailto: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] too much white matter
glad to hear it Bruce On Mon, 6 Jul 2015, Clara Kühn wrote: Hi Bruce, it worked! The surfaces now look so much better. Thanks for your help! Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 17:18:26 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, yes, it is an mp2rage image. I'm gonna work in your suggestions and see if it changes anything after rerunning the the recon-all process. Thank you! Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 16:18:06 Betreff: Re: [Freesurfer] too much white matter Hi Clara the second control point (135, 152, 163) is outside the brainmask. You will need to correct the skull stripping first. In general I wouldn't put control points in that type of location as it is certainly partial volumed. I would try something like 139, 145, 163 instead (and maybe a couple around there). Also, I assume the skull stripping failed as this is not the typical type of image we expect (since the background is so bright and noisy). Is it an mp2rage or something? There appears to be very little space between skull and brain so the stripping may be challenging, particularly in the orbitofrontal region where you had this control point (it looks like fat is shifting upwards either into or adjacent to brain) cheers Bruce On Tue, 30 Jun 2015, Clara Kühn wrote: oh, and here are the Freesurfer coordinates for the control points: 86, 143, 147 135, 152, 163 Cheers, Clara - Ursprüngliche Mail - Von: ckuehn cku...@cbs.mpg.de An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 30. Juni 2015 11:39:40 Betreff: Re: [Freesurfer] too much white matter Hi Bruce, thanks for your reply. As far as I can tell the cps are in the WM. I'd be grateful if you could take a closer look, though. You can download the dataset here: https://bigmail.cbs.mpg.de/i/2581030103b072173ff426e67d298cf4.zip Cheers, Clara - Ursprüngliche Mail - Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 29. Juni 2015 18:07:28 Betreff: Re: [Freesurfer] too much white matter Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ 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 ___ 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] Recon-all terminated abruptly
it sounds like you ran out of memory. Were other things running on the machine at the same time? How much ram does it have? On Mon, 6 Jul 2015, Park, Jung Mi wrote: Hello Freesurfer expert Recon abruptly terminated with error message from the recon-all. log: #@# Skull Stripping Mon Jul 6 13:16:25 EDT 2015 /autofs/cluster/scratch/monday/jungmi/anat_subjects/r0401AG/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) * The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed Killed Linux gencess 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s r0401AG exited with ERRORS at Mon Jul 6 13:16:52 EDT 2015 --- How can I complete recon-all -all ? Thank you in advance. J. Mi ___ 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] Recon-all terminated abruptly
Hello Freesurfer expert Recon abruptly terminated with error message from the recon-all. log: #@# Skull Stripping Mon Jul 6 13:16:25 EDT 2015 /autofs/cluster/scratch/monday/jungmi/anat_subjects/r0401AG/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) * The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed Killed Linux gencess 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s r0401AG exited with ERRORS at Mon Jul 6 13:16:52 EDT 2015 --- How can I complete recon-all -all ? Thank you in advance. J. Mi ___ 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] couple TRACULA questions
Forgot to reply re: merging. You have to merge them yourselves, sorry. On Mon, 6 Jul 2015, Harms, Michael wrote: Hi Anastasia, We are looking at running TRACULA on some data, where we were attracted by the longitudinal component of TRACULA. Is a paper on the longitudinal aspect of TRACULA in the works? If we have multiple dMRI runs/series per imaging session, do we need to merge/concatenate those ourselves prior to running trac-all? (e.g., I didn't see anything in the dmrirc config file that would allow one to provide multiple DICOM directories per subjlist/baselist entry). Also, I'm trying to get an initial sense of how much work it is going to entail to get this working in our cluster. In that regard, how customized are bedpostx_mgh and fsl_sub_mgh to the MGH cluster? Could we just modify trac-all to use the default bedpostx that comes with FSL 5.0.8, and then just modify fsl_sub to work in our cluster environment? thanks! -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu ___ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] longitudinal analysis
Hi Yawu, no, that would be the simple average. Temporal average is the linear fit (within each subject) evaluated at the mid time. So if you had 10 time points at the same day and 1 a year later, it would look like a .5 years time point. This is used to compute symmetrized percent change, representing the change with respect to the temporal average to make it more symmetric. Cheers, Martin On 07/03/2015 08:43 AM, Liu Y wrote: Dear Freesurfer experts In the command long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR, Do-avg will compute the temporal average. I do not quite understand the temporal averageIs the average of baseline and followup thicknesses? Best regards, Yawu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.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] couple TRACULA questions
Hi Anastasia, We are looking at running TRACULA on some data, where we were attracted by the longitudinal component of TRACULA. Is a paper on the longitudinal aspect of TRACULA in the works? If we have multiple dMRI runs/series per imaging session, do we need to merge/concatenate those ourselves prior to running trac-all? (e.g., I didn't see anything in the dmrirc config file thatwouldallow one to provide multiple DICOM directories per subjlist/baselist entry). Also, I'm trying to get an initial sense of how much work it isgoingto entail to get this working in our cluster. In that regard, how customized are bedpostx_mgh and fsl_sub_mgh to the MGH cluster? Could we just modify trac-all to use the default bedpostx that comes with FSL 5.0.8, and then just modify fsl_sub towork in our cluster environment? thanks! -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] couple TRACULA questions
Hi Michael - Thanks for finding longitudinal tracula attractive! :) The paper is under review. There's an ISMRM abstract that I can send you. About the cluster customization: bedpostx_mgh and fsl_sub_mgh are supersets of bedpostx and fsl_sub, so they have all the original functionality of the FSL scripts, plus a check to see if they're running on a PBS cluster and then do PBS stuff. Those additional PBS-related sections should have AY comments, but everything else from the original scripts is left intact. I'd like to give the option for trac-all to simply print out the commands, so that users can then deal by themselves with submitting them as jobs to their own clusters. Maybe I'll manage to sneak that into v6.0... Best, a.y On Mon, 6 Jul 2015, Harms, Michael wrote: Hi Anastasia, We are looking at running TRACULA on some data, where we were attracted by the longitudinal component of TRACULA. Is a paper on the longitudinal aspect of TRACULA in the works? If we have multiple dMRI runs/series per imaging session, do we need to merge/concatenate those ourselves prior to running trac-all? (e.g., I didn't see anything in the dmrirc config file that would allow one to provide multiple DICOM directories per subjlist/baselist entry). Also, I'm trying to get an initial sense of how much work it is going to entail to get this working in our cluster. In that regard, how customized are bedpostx_mgh and fsl_sub_mgh to the MGH cluster? Could we just modify trac-all to use the default bedpostx that comes with FSL 5.0.8, and then just modify fsl_sub to work in our cluster environment? thanks! -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu ___ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Data visualization
Hi FreeSurfers, I have a question regarding data visualization: Instead of presenting population average cortical thickness overlay of the right hemisphere on the right and of the left hemisphere on the left, Id like to show thickness data from epileptogenic hemisphere on one side (lets say left) and from the non-epileptogenic hemisphere on the other (lets say right). I.e. Id like to average population thickness data from mixed right and left lobes to visualize study findings in epileptogenic vs. non-epileptogenic hemispheres. Is there a neat way to accomplish this? Sincerely, David Olayinka Kamson, MD, PhD ___ 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] convert FS volume in scanner space
Dear FreeSurfers, I need to convert an FS-volume back in scanner space (to calculate overlap with manual segmentation). I went through the wiki-entry and converted to native space with mir_vol2vol, however the coordinates are still RAS and not identical with the original Scanner-coordinates. I tried mri_convert, however, the results were not as good as mri_vol2vol (apparently need trilinear interpolation, not available in mri_convert). Any help would be greatly appreciated, Cheers, Georg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA analyses in glmfit
Hi Anastasia, Thanks for the clarification. I am happy to hear that you are working on that! As the byvoxel data includes MNI coordinates, I though it could be possible to assemble them to MNI 3D space. Thanks again! Pedro Rosa. On Monday, July 6, 2015 at 12:19 PM, Anastasia Yendiki wrote: Hi Pedro - The point-wise stats from tracula are a 1D sequence of values, so they cannot be analyzed with functions that work on 2D data on the surface or 3D data in the volume. At present, you'd have to do a seperate analysis for every point along the tract. It's on my list to implement a more comprehensive and principled solution for this and will hopefully get around to it soon! BTW, the diffusion measures are extracted by tracula in the native space, not in a template space. An average path in template space is produced in case you want to visualize something on an average brain, but all the pointwise and average FA/MD/etc values are extracted in the native DWI space of each subject. Best, a.y On Sun, 5 Jul 2015, Pedro Rosa - GMail wrote: Dear Developers, Tracula’s Statistics wiki suggests one to use the statistical software of choice. Could it be glmfit? For that, I think I would need to concatenate each tract-by-voxel diffusion data from each subject (e.g., each diffusion data of course separately) in common space (e.g., MNI) and then input it to mri_glmfit / mri_glmfit-sim, whose output sig.mgh would be loaded in Freeview as a heatmap. I understood that diffusion data in Tracula is saved in .txt files, which cannot be inputed into mri_preproc or mri_label2vol. Is it possible to use glmfit with Tracula outputs? Thanks in advance, Pedro Rosa. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] convert FS volume in scanner space
Hi Georg if you have a volume (like the 001.mgz) that is in scanner coordinates you can use the reslice like and resample type flags in mri_convert: mri_convert -rl 001.mgz -rt trilinear input.mgz output.mgz cheers Bruce On Mon, 6 Jul 2015, von Polier, Georg wrote: Dear FreeSurfers, I need to convert an FS-volume back in scanner space (to calculate overlap with manual segmentation). I went through the wiki-entry and converted to native space with mir_vol2vol, however the coordinates are still RAS and not identical with the original Scanner-coordinates. I tried mri_convert, however, the results were not as good as mri_vol2vol (apparently need trilinear interpolation, not available in mri_convert). Any help would be greatly appreciated, Cheers, Georg ___ 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] isxconcat-sess
Hi Surfers and Doug, I was trying to average two scan sessions of the same subject and isxconcat-sess under dev-env failed again. This time I get this message: ERROR: cannot find /autofs/cluster/tootell/pitcairn/1/shahin/FeatureAttention_Color/Subjects2/hron1/bold/Attention_TR3_FHWM0_PR_Ver2.lh/nmask.dat Which is true! this file does not exist. Regards On Thu, May 14, 2015 at 10:39 PM, SHAHIN NASR sha...@nmr.mgh.harvard.edu wrote: Hi Doug, It works without any error. Thanks a lot On Thu, May 14, 2015 at 5:47 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: I just made a fix. Can you try it out and let me know if it works? On 05/14/2015 11:38 AM, SHAHIN NASR wrote: Hi, Does anyone know what has changed in isxconcat-sess command in nmr-dev-env? Previously I could use it to average different sessions of the same subject. But now I am getting this error: INFO: trgsubject is self, this will fail unless all sessions are the same subject ERROR: cannot find /cluster/tootell/pitcairn/1/users/good_subjects_anat//self/mri.2mm/subcort.mask.mgz Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] (no subject)
Hello Freesurfers
I meet a problem in calculate Lgi
I run fs in vituralBOX, matlab is installed. At the begining everything seems
fine .but error come in make_outer_surface. The details are in below.
=
xubuntu-VirtualBox:~ recon-all -s test001 -localGI
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rwxrwxrwx 1 fsuser fsuser 495621 Nov 17 2014
/usr/local/freesurfer/subjects/test001/scripts/recon-all.log
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14
UTC 2012 i686 i686 i386 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /Applications/freesurfer
/usr/local/freesurfer/subjects/test001/surf
#
#@# Local Gyrification Index lh Mon Jul 6 22:51:12 EDT 2015
mris_compute_lgi --i lh.pial
=
rm -Rf /usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
make_outer_surface('/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=
ERROR:: Too many arguments.
___
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] (no subject)
On the surface it seems like you moved the FS directory from one pathway to
another. If you place FS back into your applications folder, it may work. Also,
if you have Matlab 2014b or 2015a installed, it won’t work. You need
2012b-2014a for the process to run.
Hope this helps in any way.
Noah
On Jul 7, 2015, at 1:01 PM, jinyi jiny...@hotmail.com wrote:
Hello Freesurfers
I meet a problem in calculate Lgi
I run fs in vituralBOX, matlab is installed. At the begining everything seems
fine .but error come in make_outer_surface. The details are in below.
=
xubuntu-VirtualBox:~ recon-all -s test001 -localGI
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rwxrwxrwx 1 fsuser fsuser 495621 Nov 17 2014
/usr/local/freesurfer/subjects/test001/scripts/recon-all.log
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14
UTC 2012 i686 i686 i386 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /Applications/freesurfer
/usr/local/freesurfer/subjects/test001/surf
#
#@# Local Gyrification Index lh Mon Jul 6 22:51:12 EDT 2015
mris_compute_lgi --i lh.pial
=
rm -Rf
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
make_outer_surface('/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=
ERROR:: Too many arguments.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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] (no subject)
THX for your response.
I have never move fs files. but i had a MATLAB 2011b, because of the virtual
machine`s 32 bit.
May this do harm? Or I don't configure the mat lab rightly?
here is the startup.m in ~/fsuser
% FreeSurfer -%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
%-%
% FreeSurfer FAST %
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
%-%
From: noahb.markow...@gmail.com
Date: Tue, 7 Jul 2015 13:15:19 +1000
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)
On the surface it seems like you moved the FS directory from one pathway to
another. If you place FS back into your applications folder, it may work. Also,
if you have Matlab 2014b or 2015a installed, it won’t work. You need
2012b-2014a for the process to run.
Hope this helps in any way.
Noah
On Jul 7, 2015, at 1:01 PM, jinyi jiny...@hotmail.com wrote:Hello Freesurfers
I meet a problem in calculate Lgi
I run fs in vituralBOX, matlab is installed. At the begining everything seems
fine .but error come in make_outer_surface. The details are in below.
=
xubuntu-VirtualBox:~ recon-all -s test001 -localGI
WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
-rwxrwxrwx 1 fsuser fsuser 495621 Nov 17 2014
/usr/local/freesurfer/subjects/test001/scripts/recon-all.log
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14
UTC 2012 i686 i686 i386 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/local/freesurfer
Previous: /Applications/freesurfer
/usr/local/freesurfer/subjects/test001/surf
#
#@# Local Gyrification Index lh Mon Jul 6 22:51:12 EDT 2015
mris_compute_lgi --i lh.pial
=
rm -Rf /usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
reading surface from lh.pial...
writing filled volume to
/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.
=
make_outer_surface('/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/usr/local/freesurfer/subjects/test001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit
=
ERROR:: Too many arguments.
___Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe
information in this e-mail is intended only for the person to whom it
isaddressed. If you believe this e-mail was sent to you in error and the
e-mailcontains patient information, please contact the Partners Compliance
HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to
you in errorbut does not contain patient information, please contact the sender
and properlydispose of the e-mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.___
Freesurfer 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
[Freesurfer] feat statistics on surface
Hi Freesurfer experts, I am still trying to resolve the problem detailed below. It seems my version of reg-feat2anat is not working properly since it does not created the anat2exf.register.dat file needed to view fmri data analysed with FSL on the subjects native surface in FS. Doug posted a new version in response to a user about a year ago, but this seems to have been deleted/moved: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat Does someone know where I can update to this new version? Thank you! Gabriella From: Hirsch, Gabriella Sent: Monday, June 22, 2015 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: reg-feat2anat update Hi FS experts, I had a quick query I was hoping you could help with; I am trying to load functional data analyzed in FSL in Freesurfer using reg-feat2anat (http://freesurfer.net/fswiki/FsTutorial/RegisterFeatOntoAnatomical) and seem to be having the same problem as the person in this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038639.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-June/038639.html In other words, the anat2exf.register.dat file is not being created. I tried to download the new version of reg-feat2anat posted by Doug in the thread but I'm getting an error when downloading with wget: no such file reg-feat2anat Has the location of this file changed? Thank you! Best, Gabriella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] TRACULA analyses in glmfit
Hi Pedro - The point-wise stats from tracula are a 1D sequence of values, so they cannot be analyzed with functions that work on 2D data on the surface or 3D data in the volume. At present, you'd have to do a seperate analysis for every point along the tract. It's on my list to implement a more comprehensive and principled solution for this and will hopefully get around to it soon! BTW, the diffusion measures are extracted by tracula in the native space, not in a template space. An average path in template space is produced in case you want to visualize something on an average brain, but all the pointwise and average FA/MD/etc values are extracted in the native DWI space of each subject. Best, a.y On Sun, 5 Jul 2015, Pedro Rosa - GMail wrote: Dear Developers, Tracula’s Statistics wiki suggests one to use the statistical software of choice. Could it be glmfit? For that, I think I would need to concatenate each tract-by-voxel diffusion data from each subject (e.g., each diffusion data of course separately) in common space (e.g., MNI) and then input it to mri_glmfit / mri_glmfit-sim, whose output sig.mgh would be loaded in Freeview as a heatmap. I understood that diffusion data in Tracula is saved in .txt files, which cannot be inputed into mri_preproc or mri_label2vol. Is it possible to use glmfit with Tracula outputs? Thanks in advance, Pedro Rosa. ___ 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.
