Re: [Freesurfer] Question about reorienting images
Hi Timour I'll leave 1) to Doug. As for 2), the aseg.mgz is an index map into the FreeSurferColorLUT.txt (e.g. voxel value 17 means Left Hippocampus), so nearest nbr interpolation is the only kind that makes sense. Otherwise you will average index value which will give you a useless image. cheers Bruce On Tue, 9 Nov 2010, Timour Al-Khindi wrote: Hello, We are looking for a way to reorient the orig.mgz files and the segmentation (aseg.mgz) into a different plane, and we have a couple of questions. We've used tkregister2 to reorient the orig image: tkregister2 ?mov orig.mgz ?tar orig.mgz ?regheader ?reg myregister.dat myregister.dat is created by this command line. We rotate the brain in the tkregister2 gui, then save the registration. Finally, we use the mri_vol2vol command line to rotate the orig and the aseg images. For aseg.mgz: mri_vol2vol --mov aseg.mgz --targ orig.mgz --reg myregister.dat --interp nearest --o rotaseg.mgz For orig.mgz: mri_vol2vol --mov orig.mgz --targ aseg.mgz --reg myregister.dat --o rotorig.mgz This seems to look decent when we load it up in tkmedit, but we have two questions about the use of mri_vol2vol 1) Why does the algorithm need a target (won't run without it), since the transformation info is saved in myregister.dat? Also, how does it manage to work (which it does), given than neither of the targets entered are in the reoriented space? Should we use a different target? What is the role of the target? 2) A previous post specifies that interp nearest should be used to rotate the aseg.mgz file. What is the function played by that command? Should we also use it when rotating the orig.mgz file? It works without it, but do we risk distorting the image? Thanks in advance! Tim Al-Khindi ___ 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] Question about reorienting images
Hello, We are looking for a way to reorient the orig.mgz files and the segmentation (aseg.mgz) into a different plane, and we have a couple of questions. We've used tkregister2 to reorient the orig image: tkregister2 –mov orig.mgz –tar orig.mgz –regheader –reg myregister.dat myregister.dat is created by this command line. We rotate the brain in the tkregister2 gui, then save the registration. Finally, we use the mri_vol2vol command line to rotate the orig and the aseg images. For aseg.mgz: mri_vol2vol --mov aseg.mgz --targ orig.mgz --reg myregister.dat --interp nearest --o rotaseg.mgz For orig.mgz: mri_vol2vol --mov orig.mgz --targ aseg.mgz --reg myregister.dat --o rotorig.mgz This seems to look decent when we load it up in tkmedit, but we have two questions about the use of mri_vol2vol 1) Why does the algorithm need a target (won't run without it), since the transformation info is saved in myregister.dat? Also, how does it manage to work (which it does), given than neither of the targets entered are in the reoriented space? Should we use a different target? What is the role of the target? 2) A previous post specifies that interp nearest should be used to rotate the aseg.mgz file. What is the function played by that command? Should we also use it when rotating the orig.mgz file? It works without it, but do we risk distorting the image? Thanks in advance! Tim Al-Khindi ___ 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 base error
Hi Guang, yes, fixed it. The mri_concatenate_lta had difficulties reading the lta if the filename field in the lta was too long. Workaround: use short names especially for the base. There will be a fixed version of mri_concatenate_lta in the 5.1 release coming up in a few weeks. Best, Martin On Mon, 2010-11-08 at 21:06 -0600, Guang Zeng wrote: Hi, there, Last week, we met a problem when we ran the recon-all long-base pipeline. %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force %% I get the following error: mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta invert the first LTA before applying it MatrixInverse: NULL input matrix! Read individual LTAs %% Recently, my colleague found an interesting thing from several tests he did, For example, we have two subjects: 001_S_0001_2101_1_1 and 001_S_0001_2202_2_2, both of them have been processed by FreeSurfer cross-sectional pipeline. We use the following command, recon-all -base 001_S_0001_2101_1_1_to_001_S_0001_2202_2_2 -all The process will crash at the mri_concatenate_lta step I change the command to: recon-all -base 001_S_0001_2101_to_001_S_0001_2202 -tp 001_S_0001_2101_1_1 -tp 001_S_0001_2202_2_2 -all The process will crash at the mri_concatenate_lta step, again. However, if f we copied and renamed these two subjects as 001_S_0001_2101 and 001_S_0001_2202, and run the following recon-all command, recon-all -base 001_S_0001_2101_to_2202 -tp 001_S_0001_2101 -tp 001_S_0001_2202 -all It works well, no crash, So, it looks like recon-all or mri_concatenate_lta has a commandline length limit, is it true? Thanks! Guang __ From: freesurfer...@hotmail.com To: mreu...@nmr.mgh.harvard.edu CC: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] longitudinal base error Date: Fri, 29 Oct 2010 08:44:43 -0500 Hello, Martin, I checked the norm.mgz of these two time points, nothing is wrong. Maybe I can try the new version of mri_robust_register and ...template, I checked the mailing list. Actually, someone met the same kind of problem in 2009 and 2008. But it looks like this problem was unsolved. Thanks! Guang __ From: mreu...@nmr.mgh.harvard.edu Date: Thu, 28 Oct 2010 21:29:55 -0400 To: freesurfer...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] longitudinal base error Haven't seen this before. Can you send the lta file (should be in basid/MRI/transforms) Probably the lta is not correct. Also you can try to delete the base dir and rerun, maybe it was just a hiccup. Does the norm.mgz look good in the base? If not registration did not work. In that case download updated mri_robust_register and ...template (links on the wiki on the 5.0 release notes) and run again. Best Martin On 28.10.2010, at 20:24, Guang Zeng freesurfer...@hotmail.com wrote: Hi, there, %% After running this command with FS v4.5 : recon-all -base 005_S_0221BASE -tp 005_S_0221_45_20070321.105506_1 -tp 005_S_0221v2_45_20061006.104318_1 -all -force %% I get the following error: mri_concatenate_lta -invert1 005_S_0221_45_20070321.105506_1_to_005_S_0221BASE.lta identity.nofile 005_S_0221BASE_to_005_S_0221_45_20070321.105506_1.lta invert the first LTA before applying it MatrixInverse: NULL input matrix! Read individual LTAs %% Any one can help me? Thanks a lot! uang ___ 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
Re: [Freesurfer] selxavg3-sess in OSX
Does /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self.nii exist? Jason Webster wrote: I'm trying to run a retinotopic analysis with the following commands: mkanalysis-sess -analysis retino-lh -TR 2 -retinotopy 40 -paradigm rtopy.para -funcstem fmcpr.sm5.self -surface self lh -mcextreg -runlistfile retRuns -fwhm 0 selxavg3-sess -analysis retino-lh -s somesubject -df sessdir and am getting the error: /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m $Id: fast_selxavg3.m,v 1.88.2.2 2010/07/16 15:31:24 greve Exp $ outtop = /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data Extension format = nii ERROR: cannot determine format of /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self ERROR: attempting to read /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self -- ERROR: fast_selxavg3() failed\n It looks like this might have something to do with analysis.info http://analysis.info ... funcstem fmcpr.sm5.self ... RawSpace surface self lh ... Should the funcstem have gotten '.lh' or should this be worked out by getana or selxavg3-sess? Thanks, ~Jason ___ 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] Question about reorienting images
The target information is not stored in the registration file, so you have to specify it on the command-line of mri_vol2vol. I don't know what your command line was, but you have to specify a mov and a targ and a reg. Information about the reoriented space is basically stored in a combination of the reg file and the geometry in the target volume. doug Bruce Fischl wrote: Hi Timour I'll leave 1) to Doug. As for 2), the aseg.mgz is an index map into the FreeSurferColorLUT.txt (e.g. voxel value 17 means Left Hippocampus), so nearest nbr interpolation is the only kind that makes sense. Otherwise you will average index value which will give you a useless image. cheers Bruce On Tue, 9 Nov 2010, Timour Al-Khindi wrote: Hello, We are looking for a way to reorient the orig.mgz files and the segmentation (aseg.mgz) into a different plane, and we have a couple of questions. We've used tkregister2 to reorient the orig image: tkregister2 ?mov orig.mgz ?tar orig.mgz ?regheader ?reg myregister.dat myregister.dat is created by this command line. We rotate the brain in the tkregister2 gui, then save the registration. Finally, we use the mri_vol2vol command line to rotate the orig and the aseg images. For aseg.mgz: mri_vol2vol --mov aseg.mgz --targ orig.mgz --reg myregister.dat --interp nearest --o rotaseg.mgz For orig.mgz: mri_vol2vol --mov orig.mgz --targ aseg.mgz --reg myregister.dat --o rotorig.mgz This seems to look decent when we load it up in tkmedit, but we have two questions about the use of mri_vol2vol 1) Why does the algorithm need a target (won't run without it), since the transformation info is saved in myregister.dat? Also, how does it manage to work (which it does), given than neither of the targets entered are in the reoriented space? Should we use a different target? What is the role of the target? 2) A previous post specifies that interp nearest should be used to rotate the aseg.mgz file. What is the function played by that command? Should we also use it when rotating the orig.mgz file? It works without it, but do we risk distorting the image? Thanks in advance! Tim Al-Khindi ___ 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] selxavg3-sess in OSX
This file does not exist. Each retinotopy run has the files: fmcpr.sm5.self.lh.nii and fmcpr.sm5.self.rh.nii I had the impression that mkanalysis-sess and selxavg-sess had to be ran separately on the files from each hemisphere for data that had been surface smoothed in preprocessing. Is this not the case? ~Jason On Tue, Nov 9, 2010 at 9:30 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: Does /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self.nii exist? Jason Webster wrote: I'm trying to run a retinotopic analysis with the following commands: mkanalysis-sess -analysis retino-lh -TR 2 -retinotopy 40 -paradigm rtopy.para -funcstem fmcpr.sm5.self -surface self lh -mcextreg -runlistfile retRuns -fwhm 0 selxavg3-sess -analysis retino-lh -s somesubject -df sessdir and am getting the error: /Applications/freesurfer/fsfast/toolbox/fast_selxavg3.m $Id: fast_selxavg3.m,v 1.88.2.2 2010/07/16 15:31:24 greve Exp $ outtop = /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data Extension format = nii ERROR: cannot determine format of /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self ERROR: attempting to read /Users/jwebst/UW/Psych/VisCog/techAdmin/anatV1LGN/pilotData/RET/data/nsLGHa/bold/001/fmcpr.sm5.self -- ERROR: fast_selxavg3() failed\n It looks like this might have something to do with analysis.info http://analysis.info ... funcstem fmcpr.sm5.self ... RawSpace surface self lh ... Should the funcstem have gotten '.lh' or should this be worked out by getana or selxavg3-sess? Thanks, ~Jason ___ 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 ___ 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] A question about VirtualBox version of FreeSurfer Ver 5.0
Hi, there, I tried to use the VirtualBox version of FreeSurfer Ver 5.0 (I downloaded freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdi) My system is Windows 7 64-bits, the VirtualBox I am using is Version 3.2.10 r66523, I tried to select Ubuntu and Ubuntu 64-bits as the guest OS, but after I added freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdi, and ran it, a black window poped up, and says: GRUB Loading stage1.5.. GRUB loading, please wait Then it stayed there for almost an hour, and nothing happen, Anyone can help me fix this problem? Thanks alot! Guang ___ 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] -noconform flag of mri_normalize doesn't work
Dear FreeSurfers, The -noconform flag of mri_normalize doesn't seem to work properly in the centos4_x86_64_stable-pub-v5.0.0 build. I have been trying to process a volume with a native isotropic resolution of 0.7mm using recon-ll including the -cm flag to conform the input to minimum. But during the normalization of mri_normalize the volume is conformed to an isotropic resolution of 1mm. The flag is correctly used during mri_normalize, but it doesn't seem to do anything. The recon-all log says: not interpolating and embedding volume to be 256^3... But the output volume T1.mgz is conformed to 256^3 and therefore to an isotropic resolution of 1mm. This also happens if mri_normalize is used by hand using the -noconform flag. A fix is highly appreciated. Thanks in advance, Falk Lüsebrink ___ 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] Select surface vertices
Hello all, I segmented a brain with FreeSurfer and I am very satisfied about the result. After that I visualized the T1.mgz together with the white surface in TkMedit. Now I am looking for interesting anatomical structures. My goal is to assign vertices in the white surface at the corresponding points and save the coordinates or better the index of the vertices. Later I will use the selected vertices in Matlab. I already read the surface with freesurfer_read_surf.m. Do you have a good procedure to do that? I appreciate any hint. Thank you so much in advance. Sincerely, Alexander ___ 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] Select surface vertices
Hi Alexander this is probably best done by running tksurfer and tkmedit simultaneously. You can save point in tkmedit and goto point in tksurfer to find the vertex. Or you can do it in freeview, which will display the vertex directly (or you can use tkmedit-tools-find nearest vertex) cheers Bruce On Tue, 9 Nov 2010, Alexander Hunold wrote: Hello all, I segmented a brain with FreeSurfer and I am very satisfied about the result. After that I visualized the T1.mgz together with the white surface in TkMedit. Now I am looking for interesting anatomical structures. My goal is to assign vertices in the white surface at the corresponding points and save the coordinates or better the index of the vertices. Later I will use the selected vertices in Matlab. I already read the surface with freesurfer_read_surf.m. Do you have a good procedure to do that? I appreciate any hint. Thank you so much in advance. Sincerely, Alexander ___ 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] A question about VirtualBox version of FreeSurfer Ver 5.0
I think version 5.0 VDI was generated by Krish. You should check how he attached the VDI disk to Ubuntu (Sata, IDE, etc..) - Pedro Paulo de Magalhães Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom -- www.netfilter.com.br -- For mobile: http://www.netfilter.com.br/mobile On Tue, Nov 9, 2010 at 17:10, Guang Zeng freesurfer...@hotmail.com wrote: Hi, there, I tried to use the VirtualBox version of FreeSurfer Ver 5.0 (I downloaded freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdi) My system is Windows 7 64-bits, the VirtualBox I am using is Version 3.2.10 r66523, I tried to select Ubuntu and Ubuntu 64-bits as the guest OS, but after I added freesurfer-Virtualbox-linux-x86-stable-pub-v5.0.0-full.vdi, and ran it, a black window poped up, and says: GRUB Loading stage1.5.. GRUB loading, please wait Then it stayed there for almost an hour, and nothing happen, Anyone can help me fix this problem? Thanks alot! Guang ___ 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] posible error in BrainSegVol (aseg.stats) ?...
Hi: There could be an error in the computation of BrainSegVol (aseg.stats) ?... How can I check it ?... Sincerely, Gonzalo Rojas Costa ___ 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] qdec with custom paths?
Hi, My data is not in the usual SUBJECTS_DIR/fsid structure. 1. Is it possible to run qdec so that it loads each subject from a full path instead of expecting them all to be under the same SUBJECTS_DIR? ie. with something like this: qdec.table.dat path_to_fsid gender age /full/path/fsid1 Male 23 /full/otherpath/fsid2 Female 27 2. If not, do you think creating a new common subjects dir and then using symbolic links will work? 3. If not, would I have to copy the entirety of the fsid directory, or do I only need a select few subdirs like the surf/ and stats/ ? thanks, mishkin ___ 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] qdec with custom paths?
option 2. should work fine (a subjects dir with symlinks). On Tue, 2010-11-09 at 15:26 -0500, Mishkin Derakhshan wrote: Hi, My data is not in the usual SUBJECTS_DIR/fsid structure. 1. Is it possible to run qdec so that it loads each subject from a full path instead of expecting them all to be under the same SUBJECTS_DIR? ie. with something like this: qdec.table.dat path_to_fsid gender age /full/path/fsid1 Male 23 /full/otherpath/fsid2 Female 27 2. If not, do you think creating a new common subjects dir and then using symbolic links will work? 3. If not, would I have to copy the entirety of the fsid directory, or do I only need a select few subdirs like the surf/ and stats/ ? thanks, mishkin ___ 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] BrainSegVol different in wmparc and aseg
Hello, When I look at the BrainSegVol and BrainSegVolNotVent in wmparc.stats, the values are around 200,000 - 300,000. However, when I look at the same measures in aseg.stats, the values are around 1,100,000 - 1,500,000. When I sum up the individual ROIs in wmparc, it comes out to 1L. I am currently using freesurfer 4.3.1. When I look at the aseg.stats files from freesurfer 3.0.5, ran on the same subjects, the values are up around that 1 - 1.5L range. This is consistent across all of our subjects: 100 and from two different scanners at two locations. From my wmparc file: # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1774481, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1774481.00, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 243312.00, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 275688, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 275688.00, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, 1302696.178406, mm^3 My question is why would wmparc so severely underestimate the BrainSegVol measure? If I can not fix it, should I take the BrainSegVol from the aseg.stats file? Thank you! Jeff Sadino ___ 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] -noconform flag of mri_normalize doesn't work
Hi Falk, I'll try to take a look at this in the next day or two cheers Bruce On Tue, 9 Nov 2010, Falk Lüsebrink wrote: Dear FreeSurfers, The -noconform flag of mri_normalize doesn't seem to work properly in the centos4_x86_64_stable-pub-v5.0.0 build. I have been trying to process a volume with a native isotropic resolution of 0.7mm using recon-ll including the -cm flag to conform the input to minimum. But during the normalization of mri_normalize the volume is conformed to an isotropic resolution of 1mm. The flag is correctly used during mri_normalize, but it doesn't seem to do anything. The recon-all log says: not interpolating and embedding volume to be 256^3... But the output volume T1.mgz is conformed to 256^3 and therefore to an isotropic resolution of 1mm. This also happens if mri_normalize is used by hand using the -noconform flag. A fix is highly appreciated. Thanks in advance, Falk Lüsebrink ___ 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] -noconform flag of mri_normalize doesn't work
Hi Falk, I just tried it and it seemed to work for me: mri_info Gaab20070225a/mri/rawavg.mgz Volume information for Gaab20070225a/mri/rawavg.mgz type: MGH dimensions: 256 x 256 x 128 voxel sizes: 1., 1., 1.3300 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -85.1, zend: 85.1 TR: 2000.00 msec, TE: 3.44 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 1 PhEncDir: ROW ras xform present xform info: x_r = 0.5924, y_r = 0.0086, z_r = -0.8056, c_r = -9.9942 : x_a = -0.7780, y_a = -0.2537, z_a = -0.5747, c_a = 13.5548 : x_s = 0.2093, y_s = -0.9672, z_s = 0.1436, c_s = -22.2562 mri_normalize -noconform rawavg.mgz test.mgz not interpolating and embedding volume to be 256^3... reading from rawavg.mgz... normalizing image... MRInormInit: Talairach origin at (142, 110, 71) wsize 10, windows 14 above, 9 below max gradient 1.000 . . . mri_info test.mgz Volume information for test.mgz type: MGH dimensions: 256 x 256 x 128 voxel sizes: 1., 1., 1.3300 type: SHORT (4) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -85.1, zend: 85.1 TR: 2000.00 msec, TE: 3.44 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = 0.5924, y_r = 0.0086, z_r = -0.8056, c_r = -9.9942 : x_a = -0.7780, y_a = -0.2537, z_a = -0.5747, c_a = 13.5548 : x_s = 0.2093, y_s = -0.9672, z_s = 0.1436, c_s = -22.2562 On Tue, 9 Nov 2010, Falk Lüsebrink wrote: Dear FreeSurfers, The -noconform flag of mri_normalize doesn't seem to work properly in the centos4_x86_64_stable-pub-v5.0.0 build. I have been trying to process a volume with a native isotropic resolution of 0.7mm using recon-ll including the -cm flag to conform the input to minimum. But during the normalization of mri_normalize the volume is conformed to an isotropic resolution of 1mm. The flag is correctly used during mri_normalize, but it doesn't seem to do anything. The recon-all log says: not interpolating and embedding volume to be 256^3... But the output volume T1.mgz is conformed to 256^3 and therefore to an isotropic resolution of 1mm. This also happens if mri_normalize is used by hand using the -noconform flag. A fix is highly appreciated. Thanks in advance, Falk Lüsebrink ___ 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.
