Re: [Freesurfer] recon-all with FLAIR error no FSL installed
Dear Bruce, They look good to me. Should I upload a couple of them, so you can have a look? They're about 230MB each. My question is: how serious is the BBR not initializing? Should I run everything again with FSL installed? Best wishes, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: vrijdag 24 mei 2013 15:59 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] recon-all with FLAIR error no FSL installed Hi Veronica BBR can use FSL or SPM to initialize, although we'll probably add an option in the future to use some things that Martin Reuter and Christian Wachinger are working on. How did the refinement work? We've only run it on a handful of cases, so it's pretty bleeding edge and I'm interested in feedback. cheers Bruce On Fri, 24 May 2013, Popescu, Veronica wrote: Dear all, I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL installed. I do get results but there's an error message in the log file (attached) about the FSL installation missing. How bad is it? Do I have to rerun everything with FSL installed? And if so, is there any version that is preferable? Thank you very much in advance! Best wishes, Veronica 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] FMRI surface transformation for vertex-wise connectivity analysis
Hi Doug and Bruce, Doug's comment about vertex spacing and its dependence on the surface of choice has gotten me thinking: When I smooth my fMRI data using 6mm kernel, I use the command mri_surf2surf --hemi lh --s fsaverage6 --sval lh.fmri.nii.gz --cortex --fwhm-trg 6 --tval rh.fmri.nii.gz --reshape. Which surface is 6mm defined on? Is it .sphere, .white, or something else? If .sphere, do you scale the sphere so the surface area is equal to some value? Thanks, Thomas On Thu, May 16, 2013 at 11:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Ludovico, I'm not sure exactly what your pipeline is, but you should use fsaverage for vol2surf, then go from fsaverage to fsaverage4 or 5 with mri_surf2surf. The reason is that if you go directly to 4 or 5, you will miss data between the vertices. The distance between the vertices for fsaverage4 is about 5.5mm and it is about 3mm for fsaverage5, 1.4 for fsaverage6, and .7mm for fsaverage (these are all for the white surface). doug On 05/16/2013 08:58 AM, Bruce Fischl wrote: you would change fsaverage5 to fsaverage4 (fewer vertices) or fsaverage6 (more vertices) On Thu, 16 May 2013, Ludovico Minati wrote: Hi Thomas many thanks. So, in the example you have sent me, how should I go about if I wished to vary the granularity? Are there different meshes to reshape or should I generate them somehow? Ludovico On 16 May 2013 14:47, Thomas Yeo ytho...@csail.mit.edu wrote: Hi Ludovico, The mri_vol2surf example I sent you directly resample to fsaverage5, which is around 4mm spacing, resulting in 18715 vertices for both hemispheres combined after excluding the medial wall in the surfaces. I am also including the freesurfer mailing list in the email as suggested by Bruce. --Thomas On Thu, May 16, 2013 at 8:25 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ludovico I wouldn't downsample before calling mri_surf2surf. We have tools for uniformly parcellating the cortex (mris_make_face_parcellation) that can be used for this purpose after sampling the timecourses to the cortex. cheers Bruce On Thu, 16 May 2013, Ludovico Minati wrote: Hi Bruce, many thanks. Yes sorry I shall use the list from now on. But let me just ask you a clarification as we are already on these questions For our connectivity analyses, at present we parcellated in 3D volume space the cortex into a pre-set number of roughly equal volume parcels, ranging in number between around 500 to 10,000. I would need to translate this approach to the surface space in Freesurfer, i.e. be able to smooth on the cortical surface and undersample it. What is the best approach that can be used? Along this like: you wrote around 150k vertices/hemisphere. For our purposes that's an enormous number, much larger than the number of EPI voxels. How can we mesh downsample before calling mri_vol2surf? Again thanks for your kind help and patience Ludovico On 16 May 2013 14:09, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ludovico can we move this discussion to the FreeSurfer list in the future so others can answer? 1. Hard to say as sometimes one works better than the other, you'll just have to try. The transform should be rigid (6DOF) since the scalings are read from the header, why would you want affine? I think Doug has worked on this and you can specify it in the bbregister command line, but I've never used it. 2. About 150K vertices/hemisphere. They are distributed initially at 1mm spacing (the surface of the voxels), and cannot be tuned. There are some tools around for mesh downsampling if you want, and this is even easier if you go to fsaverage space (with mri_surf2surf) where we have representations based on recursive icosahedral supersamplings. 3. This is due to a bug in the initial nifti format that didn't allow any one dimension greater than 64K. If you output in .mgz it should be nvertices x 1 x 1 x ntimepoints. 4. Search for coordinate systems on our wiki. This is documented extensively. there are also matlab i/o functions for reading/writing all our formats (e.g. MRIread.m) cheers Bruce On Thu, 16 May 2013, Ludovico Minati wrote: Hi Thomas, thanks. A few quick questions, which hopefully will take little of your time but save me a lot of hassle: 1) bbregister. Do you advise using FLIRT or SPM for initialization? Is this a rigid-body transformation, or an affine one? Any way I can control the DOF? If I use SPM shall I feed the mean realigned volume here, as I expect? 2) recon-all. What is the typical number of vertices for the cortex? Any way I can control it, i.e. sample more or less finely? This would be particularly relevant for our task. 3) mri_vol2surf. Perhaps naively I was expecting an output file simply consisting of a list of values, i.e. one per vertex (assuming a single input volume that is). But the documentation says: The output will be a data set with Nv/R
[Freesurfer] mri_glmfit files
Hello all, I would just like to know what is the significance of the files that are produced after a glmfit is done. I was trying to find a write up online but I was not able to. They include : - cnr.mgh - F.mgh - gamma.mgh - gammavar.mgh - sig.mgh Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all with FLAIR error no FSL installed
Hi Veronica thanks for the offer, but I don't need to see them. Glad it seems to be working. As for BBR, I'll leave that for Doug Bruce On Mon, 27 May 2013, Popescu, Veronica wrote: Dear Bruce, They look good to me. Should I upload a couple of them, so you can have a look? They're about 230MB each. My question is: how serious is the BBR not initializing? Should I run everything again with FSL installed? Best wishes, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: vrijdag 24 mei 2013 15:59 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] recon-all with FLAIR error no FSL installed Hi Veronica BBR can use FSL or SPM to initialize, although we'll probably add an option in the future to use some things that Martin Reuter and Christian Wachinger are working on. How did the refinement work? We've only run it on a handful of cases, so it's pretty bleeding edge and I'm interested in feedback. cheers Bruce On Fri, 24 May 2013, Popescu, Veronica wrote: Dear all, I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL installed. I do get results but there's an error message in the log file (attached) about the FSL installation missing. How bad is it? Do I have to rerun everything with FSL installed? And if so, is there any version that is preferable? Thank you very much in advance! Best wishes, Veronica 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] nuintensitycor and skullstrip problems
Hi Laouchedi if you upload the dataset we'll take a look Bruce On Mon, 27 May 2013, LAOUCHEDI MAKHLOUF wrote: hi all i run recon_all on some subjects having 512x512x154 , i noticed (using tkmedit) that there are no problems with orig.mgz, and rawavg.mgz but most of them were cropped (more than half of the brain disappeared) after the -nuintensity step (nu.mgz); for one of these patients, the nu.mgz is ok but the T1.mgz produced after skullstrip is bad : the skull was largely still there on the right hemisphere. i read in the recon-all.local-copy file (in the SUBJECTS_DIR/subj/scripts folder) that we must include the -cw256 flag if the FOV is beyond 256x256x256 (just to be sure, is it the FOV -in mm- or the just the GRID). but when reading in the recon-all.log file, this step seems to be a default one when running recon_all -all command. in the recon-all.log file it is written : Original Data has (0.4883, 0.4883, 1.2) mm size and (512, 494, 154) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation 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] no hippocampal stats despite running FS 5.3 with -hippo-subfields
I can add that running the -hippo-subfields flag separately did work: recon-all -s SUBJECTIDENTIFIER -hippo-subfields Is there a reason the order of processing should matter? Is there a way I can change my recon-all call (below) so that hippo-subfields will get processed (so I do not have to make a separate call)? recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all Thank you, Sal On Sun, May 26, 2013 at 2:33 PM, Salil Soman salso...@stanford.edu wrote: Dear Freesurfer Experts, I have been running freesurfer 5.3 without any reported errors using the following command: recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all However, when I look for any of the hippocampal subfield stats (as described on http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation), I do not find any of them. Any suggestions on what I am doing incorrectly? Best wishes, Salil Soman, MD, MS ___ 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_anatomical_stats segmentation fault
Hi All, I'm running mris_anatomical_stats with a few manually defined labels. For a few of my subjects, I am getting the error: Segmentation fault on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running mri_anatomical_stats on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... reading input surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... reading input pial surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... reading input white surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... Segmentation fault Does anyone know what may be causing the Segmentation fault and what steps I should take to fix it? Thank you for your help! Rob ___ 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] nuintensitycor and skullstrip problems
hi i send you further information of the -nuintensitycor and skullstrip problem,about three control subjects. after running recon_all -i, i decided to process my data step by step, i run recon_all -autorecon1 for all of them and it ended with errors. i picked up three cases of the recon-all.log file : subject 1: #@# Nu Intensity Correction Mon May 27 18:08:32 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home_cluster/mlaouche/freesurf_makh/ctr3/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:36 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12456 /home_cluster/mlaouche/freesurf_makh/ctr3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.05, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12456/nu0.mnc... Iteration 1 Mon May 27 18:23:46 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr3/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ctr3 exited with ERRORS at Mon May 27 18:47:13 CEST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting subject 2: #@# Nu Intensity Correction Mon May 27 18:08:21 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home_cluster/mlaouche/freesurf_makh/ctr5/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:31 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12252 /home_cluster/mlaouche/freesurf_makh/ctr5/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.07, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12252/nu0.mnc... tee: ./mri_nu_correct.mni.log: Input/output error Iteration 1 Mon May 27 18:23:44 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr5/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.imp Computing ranges for each class.: . Processing:.Done Fitting splines:
Re: [Freesurfer] mri_anatomical_stats segmentation fault
Hi Rob, does the white surface look ok? How about the contents of the lh.PHC_1.label file? If both seem ok, then feel free to upload the subject and we'll figure it out Bruce On Mon, 27 May 2013, Rob Tennyson wrote: Hi All, I'm running mris_anatomical_stats with a few manually defined labels. For a few of my subjects, I am getting the error: Segmentation fault on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running mri_anatomical_stats on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... reading input surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... reading input pial surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... reading input white surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... Segmentation fault Does anyone know what may be causing the Segmentation fault and what steps I should take to fix it? Thank you for your help! Rob ___ 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] white matter volume per lobe...
Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 rh mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 lh Which commands (sintaxis) must I use to compute the white matter volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats commans with different options, but I couldn't get the volume that I need... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] Correction for multiple comparisons error
what is your cmd line? What version of FS are you using? What is the full terminal output? doug On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote: Hi! I have been running the mri_glmfit-sim command to do the correction for multiple comparisons for my group analysis and for some voxel-based thresholds (not all) there is an error that comes up when reading the colortable from the annotation file: reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** *** glibc detected *** mri_surfcluster: malloc(): memory corruption: 0x06e61230 *** and then it gets stuck. Do you happen to know what might be causing this issue? Thank you for your time, Panos ___ 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] BBR Register failing
Hi Sal, fsvol should be defined. Can you send me your fslregister? doug On 5/26/13 12:58 AM, Salil Soman wrote: Dear Freesurfer experts, WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having some problems with the fslregister script. From what I have been able to investigate. It looks like there is an issue that fsvol may not get named if you are not dealing .cor files. Code in question from fslregister script: # Use the rawavg as input (for testing only) if($fsvol == rawavg.cor) then set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz if(! -e $refvol) then # Does not exist, create set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \ --no-save-reg --regheader) echo $cmd | tee -a $LF $cmd | tee -a $LF if($status) exit 1; # Now mask it set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz set cmd = (mri_mask $refvol $brain $refvol) echo $cmd | tee -a $LF $cmd | tee -a $LF I think this lack of fsvol being named results in the errors I am getting: -- /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: ./tmp.bbregister.756/fslregister/refvol.fslregister.nii mri_convert: extra arguments (not and following) Any suggestions would be a huge help. -Sal On Sat, May 25, 2013 at 8:35 PM, Salil Soman salso...@stanford.edu mailto:salso...@stanford.edu wrote: Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Sal, can you post this to the list instead of me directly? thanks! doug On 5/25/13 11:00 PM, Salil Soman wrote: Dear Doug, I attempted to run the process we discussed earlier today for registering a different tissue contrast to the T1 after freesurfer 5.3 was run. I had run an FSSPGR for my subject using the following command: recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all It finished without any problems. Then I tried running the bbrregister command: bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold (this version was with bold contrast, but I get the same error if I try t1 or t2). The process fails and I get the following error log (below). Any suggestions on what I am doing wrong? Thanks, Sal -- Forwarded message -- From: *Salil Soman* salso...@stanford.edu mailto:salso...@stanford.edu Date: Sat, May 25, 2013 at 7:54 PM Subject: bbregister fail log To: salso...@stanford.edu mailto:salso...@stanford.edu Logfile for bbregister Sat May 25 19:51:15 PDT 2013 setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ Linux corn18.stanford.edu http://corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from QSM_906.nii.gz... TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.313177, 0.949695) k_ras = (0, -0.949695, 0.313177) writing to ./tmp.bbregister.26724/template.nii... fslregister --s WMR3T_0015z_FS --mov
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
On 5/26/13 2:11 PM, Salil Soman wrote: Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to ERROR. In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line set fsvol = brain mask (without quotes) at the beginning of the section #Convert reference to analyze the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works. see previous msg. 2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running Oh, I did not realize it was a 2D map. Why do you have a 2D map instead of 3D? That might be hard to get registered. You could have used the ADC or FA. In general, you don't want to use the contrast that you will later be testing as it creates a little bit of circularity. It is not much though, and it should be fine. 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv that maps T1 into the bold space. Is that what you want? If you want to map the bold into the anatomical space, then leave off -inv. This will also solve your problem below doug 4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats but then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat That is right, but add --t2 (since it is t2 weighted). *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff). *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add --seg-erode 1 to erode the segmentations by a voxel. This helps to prevent partial voluming. doug Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Sal, yes you can. Use bbregister to register the lowb image to the anatomical. This creates a registration matrix. Use mri_vol2vol and the registration to map the ADC map to the anatomical, then use mri_segstats to extract the values doug ps. Please post questions to the FS list instead of us directly so that others can benefit and it gets archived. thanks! On 5/25/13 1:03 PM, Salil Soman wrote: Dear Dr. Greve, Is it possible to register a nonstructural MR sequences (e.g. an ADC map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
yes On 5/26/13 4:56 PM, Salil Soman wrote: As I am working with a 3D volume and not an ADC map, should I still use --seg-erode 1 with mr segstats? Thank On Sun, May 26, 2013 at 1:11 PM, Salil Soman salso...@stanford.edu mailto:salso...@stanford.edu wrote: Hi - I realize that the --inv tag was still in my commands for mr_vol2vol (causing the target and the moving image to be swapped). Removing the --inv tag gave me a new volume normalized to aparc+aseg.nii, and so I was able to then run mri_segstats using the following command: mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_906_aparc_aseg.stats Thanks! -S On Sun, May 26, 2013 at 11:11 AM, Salil Soman salso...@stanford.edu mailto:salso...@stanford.edu wrote: Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to ERROR. In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line set fsvol = brain mask (without quotes) at the beginning of the section #Convert reference to analyze the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works. 2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv 4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats but then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat That is right, but add --t2 (since it is t2 weighted). *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff). *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add --seg-erode 1 to erode the segmentations by a voxel. This helps to prevent partial voluming. doug Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be?
Re: [Freesurfer] FMRI surface transformation for vertex-wise connectivity analysis
It is based on the white. Notice that since you are using an average subject (fsaverage6) there is some scaling that happens because an average subject will have a surface area that is much less than the average of the subjects that went into. The average of the subjects is kept when the average subject is created and used when the number of iterations is computed. doug On 5/27/13 4:13 AM, Thomas Yeo wrote: Hi Doug and Bruce, Doug's comment about vertex spacing and its dependence on the surface of choice has gotten me thinking: When I smooth my fMRI data using 6mm kernel, I use the command mri_surf2surf --hemi lh --s fsaverage6 --sval lh.fmri.nii.gz --cortex --fwhm-trg 6 --tval rh.fmri.nii.gz --reshape. Which surface is 6mm defined on? Is it .sphere, .white, or something else? If .sphere, do you scale the sphere so the surface area is equal to some value? Thanks, Thomas On Thu, May 16, 2013 at 11:48 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Ludovico, I'm not sure exactly what your pipeline is, but you should use fsaverage for vol2surf, then go from fsaverage to fsaverage4 or 5 with mri_surf2surf. The reason is that if you go directly to 4 or 5, you will miss data between the vertices. The distance between the vertices for fsaverage4 is about 5.5mm and it is about 3mm for fsaverage5, 1.4 for fsaverage6, and .7mm for fsaverage (these are all for the white surface). doug On 05/16/2013 08:58 AM, Bruce Fischl wrote: you would change fsaverage5 to fsaverage4 (fewer vertices) or fsaverage6 (more vertices) On Thu, 16 May 2013, Ludovico Minati wrote: Hi Thomas many thanks. So, in the example you have sent me, how should I go about if I wished to vary the granularity? Are there different meshes to reshape or should I generate them somehow? Ludovico On 16 May 2013 14:47, Thomas Yeo ytho...@csail.mit.edu wrote: Hi Ludovico, The mri_vol2surf example I sent you directly resample to fsaverage5, which is around 4mm spacing, resulting in 18715 vertices for both hemispheres combined after excluding the medial wall in the surfaces. I am also including the freesurfer mailing list in the email as suggested by Bruce. --Thomas On Thu, May 16, 2013 at 8:25 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ludovico I wouldn't downsample before calling mri_surf2surf. We have tools for uniformly parcellating the cortex (mris_make_face_parcellation) that can be used for this purpose after sampling the timecourses to the cortex. cheers Bruce On Thu, 16 May 2013, Ludovico Minati wrote: Hi Bruce, many thanks. Yes sorry I shall use the list from now on. But let me just ask you a clarification as we are already on these questions For our connectivity analyses, at present we parcellated in 3D volume space the cortex into a pre-set number of roughly equal volume parcels, ranging in number between around 500 to 10,000. I would need to translate this approach to the surface space in Freesurfer, i.e. be able to smooth on the cortical surface and undersample it. What is the best approach that can be used? Along this like: you wrote around 150k vertices/hemisphere. For our purposes that's an enormous number, much larger than the number of EPI voxels. How can we mesh downsample before calling mri_vol2surf? Again thanks for your kind help and patience Ludovico On 16 May 2013 14:09, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ludovico can we move this discussion to the FreeSurfer list in the future so others can answer? 1. Hard to say as sometimes one works better than the other, you'll just have to try. The transform should be rigid (6DOF) since the scalings are read from the header, why would you want affine? I think Doug has worked on this and you can specify it in the bbregister command line, but I've never used it. 2. About 150K vertices/hemisphere. They are distributed initially at 1mm spacing (the surface of the voxels), and cannot be tuned. There are some tools around for mesh downsampling if you want, and this is even easier if you go to fsaverage space (with mri_surf2surf) where we have representations based on recursive icosahedral supersamplings. 3. This is due to a bug in the initial nifti format that didn't allow any one dimension greater than 64K. If you output in .mgz it should be nvertices x 1 x 1 x ntimepoints. 4. Search for coordinate systems on our wiki. This is documented extensively. there are also matlab i/o functions for reading/writing all our formats (e.g. MRIread.m) cheers Bruce On Thu, 16 May 2013, Ludovico Minati wrote: Hi Thomas, thanks. A few quick questions, which hopefully will take little of your time but save me a lot of hassle: 1) bbregister. Do you advise using FLIRT or SPM for initialization? Is this a rigid-body transformation, or an affine one? Any way I can control the DOF? If I use SPM shall I feed the mean realigned
Re: [Freesurfer] mri_glmfit files
Look at mri_glmfit --help. The only one not explained there is cnr.mgh which is the contrasts (gamma) to residual noise stddev (rstd.mgh in the glmdir) doug On 5/27/13 4:48 AM, Joshua deSouza wrote: Hello all, I would just like to know what is the significance of the files that are produced after a glmfit is done. I was trying to find a write up online but I was not able to. They include : - cnr.mgh - F.mgh - gamma.mgh - gammavar.mgh - sig.mgh Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all with FLAIR error no FSL installed
If FSL is not installed, then bbregister should have failed and recon-all should have stopped. Did that not happen? To answer your question, it might not make any difference. If the flair and T1 were acquired at the same time, then it probably just used the scanner coordinates to do the initial alignment, which was probably pretty good. You can view the registration to see how good it is (and look at the first value in the mincost file, if that is less than .7, is is probably fine) In the end, if your surfaces look ok, then it fine. doug On 5/27/13 8:19 AM, Bruce Fischl wrote: Hi Veronica thanks for the offer, but I don't need to see them. Glad it seems to be working. As for BBR, I'll leave that for Doug Bruce On Mon, 27 May 2013, Popescu, Veronica wrote: Dear Bruce, They look good to me. Should I upload a couple of them, so you can have a look? They're about 230MB each. My question is: how serious is the BBR not initializing? Should I run everything again with FSL installed? Best wishes, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: vrijdag 24 mei 2013 15:59 To: Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] recon-all with FLAIR error no FSL installed Hi Veronica BBR can use FSL or SPM to initialize, although we'll probably add an option in the future to use some things that Martin Reuter and Christian Wachinger are working on. How did the refinement work? We've only run it on a handful of cases, so it's pretty bleeding edge and I'm interested in feedback. cheers Bruce On Fri, 24 May 2013, Popescu, Veronica wrote: Dear all, I am running FreeSurfer 5.3 with FLAIR refinement. I do not have FSL installed. I do get results but there's an error message in the log file (attached) about the FSL installation missing. How bad is it? Do I have to rerun everything with FSL installed? And if so, is there any version that is preferable? Thank you very much in advance! Best wishes, Veronica The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] white matter volume per lobe...
you will need to run mri_annotation2label and specify the output to be an annotation file instead of a segmentation. Then you will have to run mri_aparc2aseg, specifying your lobes annotation as well as --labelwm (look in the recon-all.log file for an example of how wmparc.mgz is created). Then run mri_segstats (you can also get an example from the recon-all.log file). doug On 5/27/13 5:53 PM, Gonzalo Rojas Costa wrote: Hi: I used the following commands to get the cortical volume per each lobe: mri_annotation2label --subject OAS1_0001_MR1 --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject OAS1_0001_MR1 --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_rh -b OAS1_0001_MR1 rh mris_anatomical_stats -a lobulos -f OAS1_0001_MR1_lobulos_lh -b OAS1_0001_MR1 lh Which commands (sintaxis) must I use to compute the white matter volume per each lobe ?... I tested the mri_aparc2aseg and mri_segstats commans with different options, but I couldn't get the volume that I need... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ 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] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Thank you Doug, I think I initially misinderstood a number of things about this process. I have a 3D GRE volume (I guessed its contrast is closest to BOLD, bbregister set to T1 or T2 seemed to work more poorly). It is not a 2D. I would like to transform the 3D GRE volume into freesurfer space, so mri_segstats can use the segmentations from aparc+aseg.mgz to give back mean intensity values for each anatomic area. I could not find a file called lowb.nii, and so was not sure how to proceed. 1) do I need to use the file you mentioned (lowb.nii) - and if so, where would I find the file? 2) so running mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat (note inv left off) should map the 3D volume (Vol_906.nii) into the T1 space? Thank you for all of your help. Best wishes, Sal On Mon, May 27, 2013 at 7:23 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote: On 5/26/13 2:11 PM, Salil Soman wrote: Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to ERROR. In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line set fsvol = brain mask (without quotes) at the beginning of the section #Convert reference to analyze the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works. see previous msg. 2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running Oh, I did not realize it was a 2D map. Why do you have a 2D map instead of 3D? That might be hard to get registered. You could have used the ADC or FA. In general, you don't want to use the contrast that you will later be testing as it creates a little bit of circularity. It is not much though, and it should be fine. 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv that maps T1 into the bold space. Is that what you want? If you want to map the bold into the anatomical space, then leave off -inv. This will also solve your problem below doug 4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats but then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat That is right, but add --t2 (since it is t2 weighted). *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff). *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats The input would be the adc volume mapped the anatomical space. I would use WMParcStatsLUT.txt or else you'll get a billion different areas not represented in wmparc. You may also want to add --seg-erode 1 to erode the segmentations by a voxel. This helps to prevent partial voluming. doug Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be?
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
On 5/27/13 10:42 PM, Salil Soman wrote: Thank you Doug, I think I initially misinderstood a number of things about this process. I have a 3D GRE volume (I guessed its contrast is closest to BOLD, bbregister set to T1 or T2 seemed to work more poorly). It is not a 2D. I would like to transform the 3D GRE volume into freesurfer space, so mri_segstats can use the segmentations from aparc+aseg.mgz to give back mean intensity values for each anatomic area. I could not find a file called lowb.nii, and so was not sure how to proceed. 1) do I need to use the file you mentioned (lowb.nii) - and if so, where would I find the file? You should look at the on-line tutorial for multimodal integration. I thought you were doing DTI and the lowb the the acquistion with bvalue=0. 2) so running mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat (note inv left off) should map the 3D volume (Vol_906.nii) into the T1 space? yes Thank you for all of your help. Best wishes, Sal On Mon, May 27, 2013 at 7:23 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/26/13 2:11 PM, Salil Soman wrote: Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to ERROR. In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line set fsvol = brain mask (without quotes) at the beginning of the section #Convert reference to analyze the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works. see previous msg. 2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running Oh, I did not realize it was a 2D map. Why do you have a 2D map instead of 3D? That might be hard to get registered. You could have used the ADC or FA. In general, you don't want to use the contrast that you will later be testing as it creates a little bit of circularity. It is not much though, and it should be fine. 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv that maps T1 into the bold space. Is that what you want? If you want to map the bold into the anatomical space, then leave off -inv. This will also solve your problem below doug 4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats but then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 5/25/13 1:39 PM, Salil Soman wrote: Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat That is right, but add --t2 (since it is t2 weighted). *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg Use the ADC as the moveable (not lowb, but use the lowb for bbregister). The target volume should be the T1.mgz (or any conformed volume). The output will be the adc in the anatomical space (not sure why you call it vol2diff). *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats The input would be the adc volume
