Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30091 discussions

edit or not to edit?
by Miro Drahos 17 Jan '13

17 Jan '13

Hi FreeSurfer folks, we are about to process about 120 images with FS v5.1 and stand in front of a decision whether to do manual intervention or use the results from fully-automated FS run. We intend to use the volume, thickness, area, curvature measures of subcortical and cortical regions and were hoping to receive some advice on this dilemma: /to edit / or/not to edit/? Our data is decent quality, of healthy children (6-9 years old) and adults, acquired on 3T GE scanner, FSPGR sequence, with TI=400ms, TR=8.5ms, TE=3.4ms, flip angle=15deg, resolution 0.86 x 0.86 x 1.2mm, one scan per subject. I understand that visual inspection of the results is necessary in either case. If there were gross errors detected, would you advise to exclude the subject from analysis or rather do manual editing on these subjects that need it? Any and all thoughts or comments that could help us with the decision are most appreciated! Thank you! Miro Drahos http://brainlens.org

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long_mris_slopes / mris_calc problem
by O'Shea,Andrew 17 Jan '13

17 Jan '13

Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to prepare the data using this command: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage It seems to run fine at first but after a minute or so it hits this command and crashes: mris_calc -o /Applications/freesurfer/subjects/SPIN073/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-SPIN073_lh_thickness_igG3e9/beta1.mgh div ./tmp-SPIN073_lh_thickness_igG3e9/beta0.mgh It prints: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? And then returns to my command prompt. I searched online and found someone last year asked the same question here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-September/02031… However the response links to an updated version of mris_calc but when I click the link it says I do not have permission the access. Thanks for any help in advance. -Andrew

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WM of lobes
by Gabriel Gonzalez Escamilla 17 Jan '13

17 Jan '13

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Re: [Freesurfer] A question regarding volume calculation
by Douglas N Greve 16 Jan '13

16 Jan '13

No, the subcortical calculation sums the number of voxels. For voxels on the edge of a structure, there is a partial volume calculation based on the intensity of the voxel and the mean intensities of the adjacent structures. doug On 01/16/2013 05:52 PM, KimMJ wrote: > > > ------------------------------------------------------------------------ > Dear Dr. Greve > > Thanks so much for your quick and clear response. > One additional question here. > Is this volume calculation method you have mentioned also applied to > volume measurement of subcortical GM structure (in addition to > cortical GM volume)? > > Thank you again > Kim > > > > Date: Tue, 15 Jan 2013 23:16:04 -0500 > From: greve(a)nmr.mgh.harvard.edu > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] A question regarding volume calculation > > Hi Kim, yes it is surface area times thickness. A volume at each > vertex is computed as the average area of the triangles around the > vertex times the thickness at that vertex. The volume of a > parcellation is then the sum of the volumes of the vertices in that > parcellation. > doug > > > On 1/15/13 9:03 PM, KimMJ wrote: > > Dear experts > > > I'm currently preparing a paper using the results of automatic > volumetric segmentation of subcortical and cortical grey matter > structures from aseg.stats and aparc.stats files. > I have cited previous article by Desikan RS, et al (Neuroimage > 2006;31:968-980) for the cortical GM volumetric segmentation, and > Fischl B, et al (Neuron 2002;33:341-355) for the subcortical GM > volumetric segmentation. > At this point, my question is how volumes of these structures > calculated. Is this volume of each GM structure based on surface > area multiplied by cortical thickness? > > Apology for the newbie's question. > Thank you in advance for your help. > > Kim MJ > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ Freesurfer mailing > list Freesurfer(a)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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] separate FSAverages and surface-based ROIs
by Douglas N Greve 16 Jan '13

16 Jan '13

The "annotation" is the name we give to a surface segmentation (eg, lh.aparc.annot). You can break lh.aparc.annot into its constituent label files. You can then replace the insula label file with posterior and anterior labels that you create. You can then recombine the labels back into a new annotation. Once you have the new annotation, you can run mri_aparc2aseg to map the annotation into the volume. This method will do better at filling in the cortical ribbon than mri_surf2vol or mri_label2vol. doug On 01/16/2013 01:25 PM, Paul Beach wrote: > Hi Doug, > > Thanks a lot for the reply. I'm relatively new to freesurfer and it's > great to see such a helpful community. > > I'm a little fuzzy on what you mean with your second suggestion, > related to the manual ROI creation/export to AFNI. Could you explain a > bit more about creating "a new annotation and then run mri_aparc2aseg." > > First, I'm not sure what you mean by "new annotation." > > Second, my understanding is that mri_aparc2aseg normally deals with > ROIs in the LUT. However, looking at the wiki for this command, it > seems as though I can utilize my created label using the "--annot > argName" option. > How does this look: > mri_aparc2aseg --s [subj] --annot lh.aIns.label --o lh.aIns_aparc > > > Cheers, > Paul > > > > On Wed, Jan 16, 2013 at 10:56 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Paul, > > On 01/16/2013 10:27 AM, Paul Beach wrote: > > Hello, > > > > I have two issues, currently. > > > > First, I was wondering if it would be possible to create separate > > FSAverage brains for different subject groups. I am working with > > healthy seniors and various stages of Alzheimer's disease, so > doing so > > would be very helpful from the perspective of not conflating the > > differences in neuroanatomy between the these groups. One idea > we had > > was to create separate HOME directories for each group, but we > wanted > > to know if there was an easier way. I can't find anything in the > > interwebs about this. > You can create your own fsaverage subject using make_average_subject. > Note that when you run recon-all it registers to the standard > fsaverage > space. If you want to register to a different space, you will need to > re-run mris_register. Once you do this, you will not be able to > compare > groups. > > > > Second, I utilize some ROIs that are not specified by FS (such as > > secondary somatosensory cortex and anterior vs. posterior > insula). My > > means of getting around this was to use FSAverage and tksurfer to > > hand-draw them, save them as '.label' files, map them to individual > > subjects, and export them to AFNI since much of our correlation > > analysis is done on that platform. However, I've noticed that when I > > view these hand-drawn ROIs in AFNI they only show up at the > border of > > the gray and white matter, rather than filling the entirety of the > > gray matter. Note that this problem does not occur for ROIs in the > > look up table (like the caudal ACC). Exporting these to AFNI > gives you > > a nice ROI that fills all the gray matter in the defined region. > Try using --proj frac 0 1 .1 with mri_label2vol. Or you can create > a new > annotation and then run mri_aparc2aseg. The 2nd method works a little > better since the 1st method can leave some holes. > > doug > > > > _Code I'm using_: > > For the latter problem, what I first use is mri_label2label to > map the > > fsaverage-based ROI onto individual subjects, for example with the > > left anterior insula, before using mri_label2vol: > > *mri_label2label --srclabel lh.aIns.label --srcsubject fsaverage > > --trglabel lh.aIns.label --trgsubject [subj] --regmethod surface > > --hemi lh* > > > > *mri_label2vol --label ../label/lh.aIns.label --regheader > > aparc+aseg.mgz --o gmroi_volume.nii.gz --temp orig/001.mgz* > > > > > > Then I copy the new volume file to their AFNI folder, rename it, and > > run my correlation analysis on them. > > > > Note, that for those ROIs that are in the look up table (those > > parcellated by freesurfer) I simply use mri_label2vol before > > extracting them using 3dcalc (for example, the caudal anterior > > cingulate)... > > *mri_label2vol --seg aparc+aseg.mgz --regheader aparc+aseg.mgz --o > > gmroi_volume.nii.gz --temp orig/001.mgz* > > > > *3dcalc -a gmroi_volume.nii.gz -expr 'equals(a,1002)' -prefix > > ROI_FS_lh.caudalACC.nii.gz* > > > > > > > > tl:dr > > Is it possible to "easily" create multiple FSAverages based on > > selected subjects (in my case, subject groups separated by > disease state)? > > > > and > > > > Does anyone have any advice on how to get hand-drawn surface-based > > ROIs from Freesurfer's tksurfer into AFNI that full cover the > entirety > > of the gray matter? > > > > > > Cheers and thanks! > > -- > > Paul Beach > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > -- > Paul Beach > DO/PhD candidate - Year V > Michigan State University > - College of Osteopathic Medicine - OMS V > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology > - President: American Physician Scientist Association, MSU COM Chapter -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Fwd: Re: Error with mri_vol2surf]
by Shantanu Ghosh 16 Jan '13

16 Jan '13

---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Error with mri_vol2surf From: "Shantanu Ghosh" <shantanu(a)nmr.mgh.harvard.edu> Date: Wed, January 16, 2013 2:05 pm To: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> -------------------------------------------------------------------------- Hi Doug, problem solved. I used the command: mri_vol2surf --projfrac 0.5 --src ./volstat/AC066-rh-volume.mgh \ --out ./volstat/AC066.volumefile.mgh --hemi rh --regheader 002901 \ --float2int tkregister --fixtkreg --trgsubject fsaverage Thanks Shantanu On Wed, January 16, 2013 11:02 am, Douglas N Greve wrote: > Does /volstat/AC066-rh-volume.mgh exist? > what happens when you run > ls -l /volstat/AC066-rh-volume.mgh > > doug > > On 01/16/2013 11:00 AM, Shantanu Ghosh wrote: >> Hi Freesurfers, >> >> Sorry if this is a newbie question. I receive the following error when I >> use mri_vol2surf to assign values from a subject volume file to each >> surface vertex and cant fix this ... >> >> mris_preproc command exits w/o errors in a previous step: >> mris_preproc --s AC066 --target fsaverage --hemi rh --meas volume --out >> volstat/AC066-rh-volume.mgh >> >> >> $ mri_vol2surf --projfrac 0.5 --src /volstat/AC066-rh-volume.mgh --out >> /volstat/AC066.volumefile.mgh --srcreg register.dat --hemi rh >> --float2int >> tkregister --fixtkreg >> srcvol = /volstat/AC066-rh-volume.mgh >> srcreg = register.dat >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = rh >> ProjFrac = 0.5 >> thickness = thickness >> reshape = 0 >> interp = nearest >> float2int = tkregister >> GetProjMax = 0 >> INFO: float2int on the command line (2) overrides that >> in the registration file (0). >> INFO: float2int code = 2 >> mghRead(/volstat/AC066-rh-volume.mgh, -1): could not open file >> ERROR: could not read /volstat/AC066-rh-volume.mgh as type 3 >> >> Thanks for all the help. >> Shantanu >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging

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nu_correct problem
by zach.petr＠post.cz 16 Jan '13

16 Jan '13

Dear members, when I run recon_all -subjid name -autorecon1 process stops with ERROR at nu _correct. This happens for DICOM but also IMA file type. I tried several brains. Do you have any idea what is wrong? Thanks much, Petr Zach

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Freesurfer vertex wise area reference
by MAHINDA YOGARAJAH 16 Jan '13

16 Jan '13

Dear Experts, What references can I use in a write up for the use of area measures in both vertex wise GLM and ROI based analyses. I have looked at the recommended citation blurb on the website but see nothing about specific references for area. I am using FS v5.1 with the modified mris_ preproc to facilitate qdec/GLM area analysis. Thanks. Mahinda

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Cortical thickness analysis using *.nii files
by Sinead Kelly 16 Jan '13

16 Jan '13

Dear members, I am new to Freesurfer and to cortical thickness analysis so I would like to ask a very basic question that I cannot find the answer to online - is it possible to conduct cortical thickness analysis using T1 files in *.nii format? -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Speeding up mris_fix_topology
by "Falk Lüsebrink" 16 Jan '13

16 Jan '13

Hello all, I'm processing some high resolution data with an isotropic resolution of 0.5mm and I was wondering if it would be possible to speed up mris_fix_topology somehow. Due to the increased number of vertices and also increased number of defects this stage takes incredibly long (e.g. lots of days). It would be nice if the defects are handled separately of each other to parallize the process. Maybe by first estimating and specifying the number of defects. Then by being able to run multiple instances of mris_fix_topology for the same subjects correcting one or a range of defects each. Best, Falk

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Freesurfer