Re: [Freesurfer] mri_ca_register from virtual box
I'm going to check with more ram dedicated. Many Thanks Lorenzo Busti 2011/12/5 Nick Schmansky ni...@nmr.mgh.harvard.edu 1.5GB is probably not enough. typically we recommend that recon-all have at least 3GB available to it, which can be very hard to do on a virtual machine (since windows takes 1GB, the vm linux takes another 1GB, which leaves 2GB for processes). i would setup your vm to use the maximum memory allowed (just dont run stuff in windows at the same time). n. On Mon, 2011-12-05 at 15:01 +0100, Lorenzo Busti wrote: Hi everyone I got this error while running one of my subjects mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-- #@# CA Reg Inv Thu Nov 24 05:15:42 EST 2011 /home/virtualuser/freesurfer/subjects/Petrollini2/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s Petrollini2 exited with ERRORS at Thu Nov 24 05:15:43 EST 2011 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I'm working with a virtual machine on a 32 bit computer with 4GB of RAM(2-core Intel processor 2.00 GHz). I raised the ram dedicated to the virtual machine to 1,5 GB: this is the max value permitted before the selecting bar of the virtual box changes from green to red (is it sufficent?) I have free space for data. Can you help me in solving this problem? Thanks Lorenzo Busti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Problems with mri_watershed and creating the BEM geometry file
Dear all, I have successfully run the freesurfer-steps for my subject and completed it without errors. After that I started MNE to create my BEM meshes. The manual tells me, for MNE to do that, the mri_watershed routine from freesurfer is used. Also, this runs fine, as far as the four surfaces (brain, inner_skull, outer_skull and outer_skin) are produced. Here is the problem: when MNE wants to create the BEM geometry file, it checks whether the surfaces are overlapping or not. Apparently they do: outer skin CM is 0.20 -3.31 10.19 mm Going from 5th to 4th subdivision of an icosahedron (ntri: 20480 - 5120) outer skin CM is 0.20 -3.31 10.19 mm outer skull CM is 0.20 -3.19 9.75 mm inner skull CM is 0.08 -5.38 17.14 mm Checking that outer skull surface is inside outer skin surface...[ok] Checking that inner skull surface is inside outer skull surface...[failed] Surface inner skull is not completely inside surface outer skull(sum of solid angles = -3.98566e-16 * 4*PI). Coulnd't create the geometry file Though I do not know what CM or these numbers in mm given mean, I can tell by using freeview, that the surfaces indeed overlap. My questions are now: which of all the files freesurfer created in the recon-all processes does the mri_watershed routine use? In other words, which of the surfs or transform do I have to check and manually edit to get rid of this problem? And which recon-processes do I have to run again? Is there an easier way around this problem? As always, help is very much appreciated. Thanks. Maria -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522 ___ 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 a mask from an annotation file
hi everyone i have made an annotation file from somme labels and i want to make a mask from the result (from the annotation file). i mean i want keep just the part of the brain covered by the annotation file in order to transform it by mri_convert to nifti format and make my mask. thank you for your help ___ 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 a mask from an annotation file
you can use mri_mask for this cheers Bruce On Tue, 6 Dec 2011, LAOUCHEDI MAKHLOUF wrote: hi everyone i have made an annotation file from somme labels and i want to make a mask from the result (from the annotation file). i mean i want keep just the part of the brain covered by the annotation file in order to transform it by mri_convert to nifti format and make my mask. thank you for your help ___ 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] List of midpoint talairach coordinates for each FreeSurfer cortical region?
Dear FreeSurfers, Anyone out there know of a list of talairach coordinates for FreeSurfer cortical regions (MNI? I suppose)? Thanks! Carl -- •~~•~~•~~•~~•~~•~~•~~• Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com; carl_ander...@hms.harvard.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] mri_annotation2label
Dear freesurfers, I have created labels by using the command: mri_annotation2label command (aparc.a2009s): Are these new labels only for the subject I mentioned in the last command or can I use them for other subjects aswell (e.g. in order to measure Volumetry of the auditory Cortex)? THX, Greets, Holger ___ 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] List of midpoint talairach coordinates for each FreeSurfer cortical region?
Hi Carl, Do you mean a centroid? I don't know of a list. You could run mri_annotation2label to break the annotation up into individual label files. These files are text and have XYZ in MNI305 space. You could then compute the centroid from that. doug Carl Anderson wrote: Dear FreeSurfers, Anyone out there know of a list of talairach coordinates for FreeSurfer cortical regions (MNI? I suppose)? Thanks! Carl -- •~~•~~•~~•~~•~~•~~•~~• Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfr...@gmail.com mailto:remfr...@gmail.com; carl_ander...@hms.harvard.edu mailto:carl_ander...@hms.harvard.edu •~~•~~•~~•~~•~~•~~•~~• ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] mri_annotation2label
Only for the subject specified on the command line. doug Klein, Holger wrote: Dear freesurfers, I have created labels by using the command: mri_annotation2label command (aparc.a2009s): Are these new labels only for the subject I mentioned in the last command or can I use them for other subjects aswell (e.g. in order to measure Volumetry of the auditory Cortex)? THX, Greets, Holger ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Contrasts in GLM
In this case you have 4 class variables and 3 continuous, so you'll have 16 regressors (and so 16 elements in your contrast). Your actual contrast vector depends on the order of your class variables in the fsgd. Assuming that the order is MP, FP, MV, FV, then the regressors will have the following meaning: 1. MP-Offset 2. FP-Offset 3. MV-Offset 4. FV-Offset 5-8. Age-Slope 9-12. MMSE-Slope 13-16. Ed-Slope The contrast you list below would then compute the average thickness of the volunteers, probably not what you want. But I'm not sure what contrast you actually want (not clear from see if they affect thickness). Can you be more specific/precise? doug Linda Zhang wrote: Hi Doug, Sure, my fsgd file contained two groups originally, M and F. I had three continuous variables, which were Age, MMSE, Education. I wanted to test whether thickness is correlated with MMSE scores after controlling for gender, age and education. I now want to add two more class variables (patient and volunteer), and see if they affect thickness. My question was asking if the contrasts in this case would be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? I tried mris_preproc again with a different group, and that worked fine, so maybe it was just a fluke. Thanks! Cheers, Linda On 5 December 2011 23:10, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Linda Zhang wrote: Hi Doug, Thanks for the clarification. If I were to add another two class variables (patient and subject, for example) and I wanted to see if they affected thickness, assuming they come after gender in the fsgd file, would the contrasts then be [0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0]? Sorry, I can't remember what your design is (I answer a lot of emails and they often blend together). Can you refresh my memory? From the powerpoint slides, there's an example where two contrast matrices are used (age, gender), what kind of output would that produce? It would produce results (p-values, eg) for each of the contrasts. This allows you to run one command instead of one for each contrast. /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh doesn't exist, I'm not sure why... Your mris_preproc failed or you are not in the directory that has this file. doug Cheers, Linda On 3 December 2011 01:26, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: does /home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh exist? doug Linda Zhang wrote: Dear all, I think I figured out the contrasts (I'm using [0 0 0 0 0.5 0.5 0 0]...is that correct?) but I've come across an error when trying to do the next step in the tutorial. I didn't cache the data during recon-all, so I ran the following: mris_preproc --fsgd MMSE-AD.fsgd --target fsaverage --hemi lh --meas thickness --out lh.MMSE-AD.thickness.00.mgh It seemed to run smoothly (I've attached the log below) so I ran the next step: mri_surf2surf --hemi lh --s fsaverage --sval lh.MMSE-AD.thickness.00.mgh --fwhm 10 --cortex --tval lh.MMSE-AD.thickness.10.mgh I got the following error: Reading source surface reg /home/virtualuser/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Loading source data mghRead(/home/virtualuser/freesurfer/subjects/lh.MMSE-AD.thickness.00.mgh, -1): could not open file ERROR: could not read lh.MMSE-AD.thickness.00.mgh as type 3 Can anyone tell me where the problem is? Thanks! Cheers, Linda The log for mris_preproc (truncated to the last subject and last line): --- #@# 12/12 avo1249 Fri Dec 2 18:20:04 HKT 2011 -- --- mri_surf2surf --srcsubject avo1249 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.18275/avo1249.12.mgh --sval /home/virtualuser/freesurfer/subjects/avo1249/surf/lh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target
[Freesurfer] mri_surf2surf error - Return code 254
Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype= trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john ___ 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] mri_surf2surf error - Return code 254
Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffi...@gmail.com wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype = trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john ___ 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] mri_surf2surf error - Return code 254
What is lh.pial_converted.mgz? How big is it? what do get if you run mri_info on it? doug John Griffiths wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype= trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] mri_surf2surf error - Return code 254
surf2surf actually takes surface overlays (not surfaces themselves) as input, and they can be in any format that FS reads. The wiki is probably not up-to-date as those options are ok. doug Daniel Wakeman wrote: Hi John, It seems weird that you are using .mgz files (this suffix is for volume files) with mri_surf2surf (whose inputs should be surfaces). Also, it seems that several of the options you are trying I don't believe exist at least according to the wiki (e.g. -cortex -fwhm). Are you sure you are using the right command? D On Tue, Dec 6, 2011 at 1:28 PM, John Griffiths j.davidgriffi...@gmail.com wrote: Dear list, I am having the following memory allocation problem when running mri_surf2surf. Can't find any mention of this error on the list or the internet - sorry if I've missed anything. mri_surf2surf --cortex --fwhm 5. --hemi lh --sval /home/jdg45/lh.pial_converted.mgz --tval /home/jdg45/CBU070282_smoother_surf.mgz --s CBU070282 Standard output: srcsubject = CBU070282 srcval = /home/jdg45/lh.pial_converted.mgz srctype= trgsubject = CBU070282 trgval = /home/jdg45/CBU070282_smoother_surf.mgz trgtype= srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi= lh trghemi= lh frame = 0 fwhm-in= 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /work/imaging5/Freesurfer/CBU070282/surf/lh.sphere.reg Loading source data Standard error: MRIalloc: could not allocate 2032167524 slices Cannot allocate memory Return code: 254 Any suggestions? Thanks, john ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Diffusion Tutorial and GroupAnalysis.csh
Dear All, 1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the following scrip: GroupAnalysis.csh with the following instruction: # Assemble input for group analysis set type = CVS-to-avg35# alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' Can you please explain what means TAL-to-avg35 if my DTI data (FA) is by default registered on the TAL space and I got the file fa-tal.nii? How I can get the TAL-to-avg35 template? Is this different than the one on which my data was registered by default? 2) I was trying to find an explanation for the color map: Min, Mid, Max and Offset values in Free View. Can someone please explain me if I have the color map set it up as HEAT what is the meaning of the above values if for example I am viewing the existing clusters after multiple comparison for the DTI data. 3) Can I load my FA group data registered on TAL: group-fa-tal.nii with tkmedit? Many thanks. Antonella___ 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] [FreeSurfer]: mkanalysis-sess
Hi Doug, It seems that there are still problems related to using -per-session. Preproc-sess now finishes apparently fine (correct file names are generated, i.e., fmc.*) but the analyses again defaults to using -per-run at mkanalysis-sess. Specifically, mkanalysis-sess creates an analysis.info file (attached) where the parameters mcstem and nuisreg still point to -per-run (mcstem fmcpr and nuisreg mcprextreg 3). Consequently the rest of the analysis fails. I have attached the analysis.info file in the email Thank you for your help again! -Tapsya Details: Machine: adapt nmr-dev-env (vs 5.1) preproc-sess -s avml07 -surface faverage lhrh -mni305 -per-session -so siemens -fsd bold -fwhm 5 set ana_BASIC_lh = ISIXTR_BERT_ERFIRsm5pf5tpefsub_18cat_lh mkanalysis-sess -analysis $ana_BASIC_lh -surface fsaverage lh -fwhm 5 -TR 1.15 -paradigm AVML_BRERT_ISIXTR_001_18cat.par -event-related -nconditions 18 -fir 2.3 18.4 -mcextreg -polyfit 5 -runlistfile rlf_ISIXTR_BERT.txt -stc siemens -force -fsd bold -tpef tpef.txt --- I just ran this co mmand and it completed successfully preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm 5 Is this what you ran? I'm also running it to generate the surfaces now, but it does not seem to be complaining. doug Douglas N Greve wrote: I'm currently running preproc-sess -s avml07 -mni305 -per-session -so siemens -fsd bold -fwhm 5 and it seems to be going ok, I won't know until tomorrow whether this is really working or not doug r...@nmr.mgh.harvard.edu wrote: Still no luck. mc-sess is stubbornly using -per-run despite that the preproc-sess requests per-sess. This may be where things get on the wrong track. -Tommi Sorry, what I meant was for you to change the name and then run the stream as usual. doug r...@nmr.mgh.harvard.edu wrote: Done. I also made a backup of the registration. The entire directory at /space/adapt/1/users/raij/AVISI_FSFAST5.1/ is a copy of the actual data residing elsewhere (apart from the Freesurfer recons) so feel free to change anything you need. -Tommi I think I've found the problem, but it's going to be a bit difficult to fix. Can you change the name of your registration file to register.dof6.dat and remove write permissions so that it does not get overwritten? doug r...@nmr.mgh.harvard.edu wrote: Yes we have. It exits with the same error as below. -Tommi Have you tried specifying your regfile with -regfile? doug r...@nmr.mgh.harvard.edu wrote: Hi Doug, Thank you for your help today! I tried running preproc-sess again but it again exits with per-session related errors. However, the errors are different than before so I think the changes you made were a step to the right direction. This time preproc-sess \ -sf subjectname \ -df sessdir \ -mni305 \ -per-session \ -sliceorder siemens \ -fsd bold \ -fwhm 5 \ -surface $SUBJECT lhrh \ -noreg \ # I want to use my manually adjusted bold/register.dof6.dat file (1) mc-sess output is still saved with the per-run stem (pr) despite that we defined -per-session. (2) stc-sess output is still saved with the per-run stem (pr) despite that we defined -per-session. (3) rawfunc2surf-sess defaults to -per-run and then expects to find instem fmcpr.siemens (4) ERROR: cannot find /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/register.dof6.dat. Apparently the script looks for the registration file inside the run directory (as it should for per-run analysis) instead of the fsd bold where it should reside for a -per-session analysis. This forces the script to exit. I changed permissions so that you can write in the study directory. For details please see below. Thanks! -Tommi Tapsya on machine avml nmr-dev-env (vs 5.1) cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs setenv SUBJECT avml07 logs in /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07/log preproc-sess log file $Id: preproc-sess,v 1.48 2011/11/14 17:41:35 greve Exp $ raij setenv FREESURFER_HOME /usr/local/freesurfer/dev setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs Linux avml 2.6.32-131.12.1.el6.x86_64 #1 SMP Mon Sep 26 10:13:43 BST 2011 x86_64 x86_64 x86_64 GNU/Linux /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07 /usr/local/freesurfer/dev/fsfast/bin/preproc-sess -sf subjectname -df sessdir -mni305 -per-session -sliceorder siemens -fsd bold -fwhm 5 -surface avml07 lhrh -noreg Mon Nov 14 20:07:57 EST 2011 instem f mc 1 f fmcpr stc 1fmcpr fmcpr.siemens sm 0 mask 1 brain Original Message Subject: [FreeSurfer]: preproc-sess error From:tap...@nmr.mgh.harvard.edu Date:Thu, November 10, 2011 1:41 pm To: freesurfer@nmr.mgh.harvard.edu Cc: r...@nmr.mgh.harvard.edu
[Freesurfer] Bad registration
Dear All: I was using dtrecon on my DTI data and by default it will register my diffusion data (fa) on the TAL space so i got the fa-tal.nii file and the fa-tal-nii.reg the file which encodes the transformation while registering to the TAL space. Can you please advise me what is the best way to check if my registration is good or bad? Thank you. Antonella ___ 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] Diffusion Tutorial and GroupAnalysis.csh
Hi Antonella, 1) On the FS Diffusion Tutorial webpage I found for the Group Analysis the following scrip: GroupAnalysis.csh with the following instruction: # Assemble input for group analysis set type = CVS-to-avg35# alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' Can you please explain what means TAL-to-avg35 if my DTI data (FA) is by default registered on the TAL space and I got the file fa-tal.nii? How I can get the TAL-to-avg35 template? Is this different than the one on which my data was registered by default? There is probably a typo in the tutorial. It should read # alternatively could be 'TAL' or 'MNI' You can replace the mri_cvs_registered files with any other tools output that you want to use for your final comparison. 3) Can I load my FA group data registered on TAL: group-fa-tal.nii with tkmedit? Yes, you shoud and also with Freeview. Lilla ___ 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] trctrain/trainlist
Hi, I am using TRACULA for the first time, and I am having trouble locating $FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal subjects to enter in for set trainfile command. This is what my Freesurfer home directory looks like: cpdla@ba3:/software/Freesurfer/5.0.0$ ls ASegStatsLUT.txt FreeSurferColorLUT.txt SegmentNoLUT.txt AUTHORS FreeSurferEnv.csh sessions average FreeSurferEnv.shSetUpFreeSurfer.csh bin fsafd SetUpFreeSurfer.sh build-stamp.txt fsfast Simple_surface_labels2009.txt DefectLUT.txt lib subjects diffusion matlab tkmeditParcColorsCMA docs mni WMParcStatsLUT.txt. Is there a way I can get this file? Thanks for the help in advance. Sorry for the confusion. -C. Paula ___ 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] trctrain/trainlist
Hi - It's $FREESURFER_HOME/trctrain/trainlist.txt. Note the underscore. In any case this is the default, so you don't have to specify trainfile in your dmrirc unless you're using something else. a.y On Tue, 6 Dec 2011, C. Paula de los Angeles wrote: Hi, I am using TRACULA for the first time, and I am having trouble locating $FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal subjects to enter in for set trainfile command. This is what my Freesurfer home directory looks like: cpdla@ba3:/software/Freesurfer/5.0.0$ ls ASegStatsLUT.txt FreeSurferColorLUT.txt SegmentNoLUT.txt AUTHORS FreeSurferEnv.csh sessions average FreeSurferEnv.sh SetUpFreeSurfer.csh bin fsafd SetUpFreeSurfer.sh build-stamp.txt fsfast Simple_surface_labels2009.txt DefectLUT.txt lib subjects diffusion matlab tkmeditParcColorsCMA docs mni WMParcStatsLUT.txt. Is there a way I can get this file? Thanks for the help in advance. Sorry for the confusion. -C. Paula ___ 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] trctrain/trainlist
i dont think those files are in v5.0.0. you will need to download v5.1. n. On Tue, 2011-12-06 at 17:12 -0500, C. Paula de los Angeles wrote: Hi, I am using TRACULA for the first time, and I am having trouble locating $FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal subjects to enter in for set trainfile command. This is what my Freesurfer home directory looks like: cpdla@ba3:/software/Freesurfer/5.0.0$ ls ASegStatsLUT.txt FreeSurferColorLUT.txt SegmentNoLUT.txt AUTHORS FreeSurferEnv.csh sessions average FreeSurferEnv.shSetUpFreeSurfer.csh bin fsafd SetUpFreeSurfer.sh build-stamp.txt fsfast Simple_surface_labels2009.txt DefectLUT.txt lib subjects diffusion matlab tkmeditParcColorsCMA docs mni WMParcStatsLUT.txt. Is there a way I can get this file? Thanks for the help in advance. Sorry for the confusion. -C. Paula ___ 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] trctrain/trainlist
Oh yeah, that too. Tracula came out in 5.1. On Tue, 6 Dec 2011, Nick Schmansky wrote: i dont think those files are in v5.0.0. you will need to download v5.1. n. On Tue, 2011-12-06 at 17:12 -0500, C. Paula de los Angeles wrote: Hi, I am using TRACULA for the first time, and I am having trouble locating $FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal subjects to enter in for set trainfile command. This is what my Freesurfer home directory looks like: cpdla@ba3:/software/Freesurfer/5.0.0$ ls ASegStatsLUT.txt FreeSurferColorLUT.txt SegmentNoLUT.txt AUTHORS FreeSurferEnv.csh sessions average FreeSurferEnv.shSetUpFreeSurfer.csh bin fsafd SetUpFreeSurfer.sh build-stamp.txt fsfast Simple_surface_labels2009.txt DefectLUT.txt lib subjects diffusion matlab tkmeditParcColorsCMA docs mni WMParcStatsLUT.txt. Is there a way I can get this file? Thanks for the help in advance. Sorry for the confusion. -C. Paula ___ 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.
Re: [Freesurfer] trctrain/trainlist
thanks! it worked when i updated to 5.1 On Tue, Dec 6, 2011 at 6:13 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Oh yeah, that too. Tracula came out in 5.1. On Tue, 6 Dec 2011, Nick Schmansky wrote: i dont think those files are in v5.0.0. you will need to download v5.1. n. On Tue, 2011-12-06 at 17:12 -0500, C. Paula de los Angeles wrote: Hi, I am using TRACULA for the first time, and I am having trouble locating $FREESURFER/HOME/trctrain/**trainlist.txt..of 33 normal subjects to enter in for set trainfile command. This is what my Freesurfer home directory looks like: cpdla@ba3:/software/**Freesurfer/5.0.0$ ls ASegStatsLUT.txt FreeSurferColorLUT.txt SegmentNoLUT.txt AUTHORS FreeSurferEnv.csh sessions average FreeSurferEnv.shSetUpFreeSurfer.csh bin fsafd SetUpFreeSurfer.sh build-stamp.txt fsfast Simple_surface_labels2009.txt DefectLUT.txt lib subjects diffusion matlab tkmeditParcColorsCMA docs mni WMParcStatsLUT.txt. Is there a way I can get this file? Thanks for the help in advance. Sorry for the confusion. -C. Paula __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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] dt_recon error
Hello, I'm having a problem with dt_recon on data scanned by Siemens TrioTim. I'm using v4.5.0, with Mac OS 10.6.8. dt_recon ran for a while, and stopped with an error ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat I found the same errors reported to this mailing list, but found no solution. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019755.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07935.html In YDTI/YD11A/ folder, I have the following files dt_recon.log dwi-ec.ecclog dwi-ec.nii dwi-infodump.dat dwi.nii mri_glmfit.log In dwi-infodump.dat, I see bunch of lines, but I don't see sWiPMemBlock.alFree. Please help! Thanks, Yuko Yotsumoto #@#--- Fitting Tensors Wed Dec 7 10:15:52 JST 2011 cd /Users/yuko/Documents/FreeSurfer/subjects mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ cwd /Users/yuko/Documents/FreeSurfer/subjects cmdline mri_glmfit --y /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii --glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A --dti /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat sysname Darwin hostname Yukos-iMac.local machine i386 user yuko FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii logyflag 1 X/Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat usedti 1 glmdir /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A IllCondOK 0 DoFFx 0 Creating output directory /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A Loading y from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-ec.nii Using DTI bValue = 700 ERROR: cannot extract sWiPMemBlock.alFree[8] from /Users/yuko/Documents/FreeSurfer/sessions/YDTI/YD11A/dwi-infodump.dat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tracula ERROR: must specify brain mask volume for output subject
Hi. I am running into the following error: ERROR: fio_pushd: /mindhive/gablab/users/cpdla/Documents//s1001/dlabel/mni ERROR: must specify brain mask volume for output subject . I googled this error and it seems like you suggested this to someone else : As for your error, it looks like maybe the freesurfer recon wasn't found, so it skipped some steps (diffusion-to-anatomical registration and mask creation). Does the freesurfer recon dir /home/ajfurst/Data/WRIISC/014/ exist? a.y What is the freesurfer recon dir supposed to look like? Any suggestions on how to fix this error? Below is my output. Thanks, C. Paula ba3:~/Documents trac-all -prep -c dmrirc_single_subject set: Variable name must begin with a letter. INFO: SUBJECTS_DIR is /mindhive/gablab/users/cpdla/Documents/diffusion_recons INFO: Diffusion root is /mindhive/gablab/users/cpdla/Documents/ Actual FREESURFER_HOME /software/Freesurfer/5.1.0 trac-preproc -c /mindhive/gablab/users/cpdla/Documents//s1001/scripts/dmrirc.local -log /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.log -cmd /mindhive/gablab/users/cpdla/Documents//s1001/scripts/trac-all.cmd #- /software/Freesurfer/5.1.0//bin/trac-preproc #- #@# Image corrections Tue Dec 6 22:02:37 EST 2011 mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz mri_convert /data/memory/sourcemem//s1001/156000-20-1.dcm /mindhive/gablab/users/cpdla/Documents//s1001/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /data/memory/sourcemem//s1001/156000-20-1.dcm... Getting Series No INFO: Found 3207 files in /data/memory/sourcemem//s1001 INFO: Scanning for Series Number 20 Scanning Directory INFO: found 35 files in series INFO: loading series header info. RunNo = 19 WARNING: Run 1 appears to be truncated Files Found: 35, Files Expected (lRep+1): 60 FileName /data/memory/sourcemem//s1001/156000-20-1.dcm Identification NumarisVersyngo MR B15 ScannerModel TrioTim PatientName Gab_source_s1001 Date and time StudyDate 20091119 StudyTime 170216.156000 SeriesTime180621.328000 AcqTime 180331.855000 Acquisition parameters PulseSeq ep_b0#1 Protocol DIFFUSION_HighRes_Short PhEncDir COL EchoNo1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime7980 PhEncFOV 256 ReadoutFOV256 Image information RunNo 19 SeriesNo 20 ImageNo 1 NImageRows1024 NImageCols1024 NFrames 35 SliceArraylSize 64 IsMosaic 1 ImgPos863.3041 1153.2142 -113.6526 VolRes 2. 2. 2. VolDim128 128 64 Vc -0.9895 -0.1445 0.0066 Vr 0.1446 -0.9873 0.0662 Vs -0.0031 0.0664 0.9978 VolCenter 0. 0. 0. TransferSyntaxUID unknown INFO: sorting. INFO: (128 128 64), nframes = 35, ismosaic=1 Could not parse NUMARIS version string syngo MR B15 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 7980, TR = 7980 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix - 0.989 -0.141 0.034 4.549; 0.145 0.949 -0.279 4.841; 0.007 0.281 0.960 24.557; 0.000 0.000 0.000 1.000; This looks like an MGH DTI volume MGH DTI SeqPack Info 0 ep_b0#1 0.00 1 1 ep_b0#2 0.00 2 2 ep_b0#3 0.00 3 3 ep_b0#4 0.00 4 4 ep_b0#5 0.00 5 5 ep_b700#1 700.00 1 6 ep_b700#2 700.00 2 7 ep_b700#3 700.00 3 8 ep_b700#4 700.00 4 9 ep_b700#5 700.00 5 10 ep_b700#6 700.00 6 11 ep_b700#7 700.00 7 12 ep_b700#8 700.00 8 13 ep_b700#9 700.00 9 14 ep_b700#10 700.00 10 15 ep_b700#11 700.00 11 16 ep_b700#12 700.00 12 17 ep_b700#13 700.00 13 18 ep_b700#14 700.00 14 19 ep_b700#15 700.00 15 20 ep_b700#16 700.00 16 21 ep_b700#17 700.00 17 22 ep_b700#18 700.00 18 23 ep_b700#19 700.00 19 24 ep_b700#20 700.00 20 25 ep_b700#21 700.00 21 26 ep_b700#22 700.00 22 27 ep_b700#23 700.00 23 28 ep_b700#24 700.00 24 29 ep_b700#25 700.00 25 30 ep_b700#26 700.00 26 31 ep_b700#27 700.00 27 32 ep_b700#28 700.00 28 33 ep_b700#29 700.00 29 34 ep_b700#30 700.00 30 bValue = 700 nB0 = 5 nDir = 30 GradFile /software/Freesurfer/5.1.0//diffusion/mgh-dti-seqpack/gradient_mgh_dti30.gdt FileName /data/memory/sourcemem//s1001/156000-20-35.dcm Identification NumarisVersyngo MR B15 ScannerModel TrioTim PatientName Gab_source_s1001 Date and time StudyDate 20091119 StudyTime 170216.156000
Re: [Freesurfer] mri_glmfit-sim error with v5.0
Thank you Doug, Hi Yuko, I think you must have an older version of glmfit-sim some how. I've put a newer version here: I replaced the /bin/mri_glmfit-sim, but got the same error. [ERROR 1] In line 292: set csdCache = $CacheDir/$subject/$hemi/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd In stead of making csdCache = /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd it did csdCache = /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd It looks like I failed to tell freesurfer that $subject=fsaverage and $hemi=lh. I changed this line to: set csdCache = $CacheDir/fsaverage/lh/$CacheLabel/fwhm$fwhmStr/$simsign/th$threshStr/mc-z.csd and this worked. But I still don't understand why I got the error with mri_glmfit-sim. [ERROR 2] In line 93, anattype is set to volume, but I'm doing surface analysis. set anattype = volume; Changing this to set anattype = surface; worked, but does this mean mri_glmfit-sim is specialized for volume analysis only? Is there a way to change this in the command line not in the original code? Best, Yuko Hi Yuko, I think you must have an older version of glmfit-sim some how. I've put a newer version here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim-v5.0 copy this to your $FREESURFER_HOME/bin/mri_glmfit-sim (ie, change the name; and make a backup copy). doug On Nov 23, 2011, at 2:07 PM, yukoyy wrote: Hello I'm having a trouble with mri_glmfit-sim with v5.0, which is locally installed on Mac 10.6.8. Whan I ran: mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166 I got: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd I have /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd in my directory. It looks like I need to somehow tell freesurfer /fsaverage/lh/, but how? Before mri_glmfit-sim, I did the followings: isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh -c 16vs4 -o MPgroup mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz % - Also, when I did: mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite I got several warnings and errors (full error message pasted at the end of this email): cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz WARNING: unrecognized mri_glmfit cmd option --surface WARNING: unrecognized mri_glmfit cmd option fsaverage WARNING: unrecognized mri_glmfit cmd option lh WARNING: unrecognized mri_glmfit cmd option --nii.gz mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii Bus error I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? When I paste mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz in the command line, it works without any error. Thanks in advance! Yuko Yotsumoto % full error message regarding the second question --- cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz WARNING: unrecognized mri_glmfit cmd option --surface WARNING: unrecognized mri_glmfit cmd option fsaverage WARNING: unrecognized mri_glmfit cmd option lh WARNING: unrecognized mri_glmfit cmd option --nii.gz log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log cd /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4 /Applications/freesurfer/bin/mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite $Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $ Wed Nov 23 13:55:01 JST 2011 Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 kawabata setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 15.248189 nSimPerJob = 100 1/1 Wed Nov 23 13:55:01 JST 2011 mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2
