Re: [Freesurfer] hello freesurfer developer~
On 08/10/2015 10:06 PM, A-reum Min wrote: HI expert ! My name is Areum. I have some question to you. 1. Does FreeSurfer offer a effect size? if that offer, how can i use effect size? If you're doing a group analysis, you can compute fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o glmdir/contrast/effectsize.mgh 2. I was wondering about the stats.dat file in stats_table (in Qdec folder). Stats.dat file’s value mean that each area’s average (include whole vertex) or each area’s average (only significant vertex)? what stats.dat? if subject/stats/lh.aparc.stats, then the area is the total area for the ROI 3. Can I get whole vertex value or significant vertex value? Because, I want to compare two groups correlation using SPSS. In addition, I want to compare thickness, volume and surface area correlation within the one group using SPSS. You can extract a given vertex with mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf vertexno.dat vertexno.dat will be a text file with number of rows equalt to thge number of subjects where the value is the data from the given (0-based) vertex no. y.mgh is the input to mri_glmfit 4. I currently use the default cluster size(significant area threshold is 0mm^2). So, I want to control cluster size larger than default cluster size. How can I control the cluster size? I don't know what you mean. 5. In FreeSurfer manual, GLM and Qdec have a same results. But when I use the both(GLM, Qdec) group analysis program results are not same. What is differences between two analysis program? How can I get same result while GLM and Qdec? No way to know unless you tell us the specifics of what you did 6. How can I get surface area and volume using GLM(group analysis program)? surface area and volume are outputs of recon-all, not glm plz reply to me 2015-08-10 21:35 GMT+09:00 A-reum Min naniy...@gmail.com mailto:naniy...@gmail.com: Hello developer~ I have some questions to you. 1. Does FreeSurfer offer a effect size? if that offer, how can i use effect size? 2. I was wondering about the stats.dat file in stats_table (in Qdec folder). Stats.dat file’s value mean that each area’s average (include whole vertex) or each area’s average (only significant vertex)? 3. Can I get whole vertex value or significant vertex value? Because, I want to compare two groups correlation using SPSS. In addition, I want to compare thickness, volume and surface area correlation within the one group using SPSS. 4. I currently use the default cluster size(significant area threshold is 0mm^2). So, I want to control cluster size larger than default cluster size. How can I control the cluster size? 5. In FreeSurfer manual, GLM and Qdec have a same results. But when I use the both(GLM, Qdec) group analysis program results are not same. What is differences between two analysis program? How can I get same result while GLM and Qdec? 6. How can I get surface area and volume using GLM(group analysis program)? thanks for your help 2015-07-27 14:28 GMT+09:00 A-reum Min naniy...@gmail.com mailto:naniy...@gmail.com: Hello bruce I solve this problem(12.png) Thank you 2015-07-27 13:03 GMT+09:00 dgw dgwake...@gmail.com mailto:dgwake...@gmail.com: Hi A-reum, I think you may be able to get a faster response if you include some details about your setup: I would start with the following: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting and run bugr. hth D On 7/26/15 5:17 PM, A-reum Min wrote: Hi, Bruce When i use a Qdec, this message(12.png) show up.. How can i solve this problem? 2015-07-23 22:57 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu: 1. No, each subject has a different #. You can map to fsaverage (this is what -qcache does if you specify it for recon-all), then they will have the same #. 2. What result data do you mean? 3. Yes, although I'll leave the details to Doug (since I don't remember how his cluster code works). 4. The significance doesn't depend on the cluster size unless you do multiple comparison corrections (and even then only if you do them a certain way)
Re: [Freesurfer] FW: Permutation output
look in the folder of one of the contrasts (eg, rh-Diff-BD-HC-Intercept-sulc). Also, if you can paste such text into the email it is much more convenient for us than to sent us a tiff On 08/12/2015 11:12 AM, pablo najt wrote: Dear FS exp, In case my message got swamped, I am reposting my question. Many thanks! Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 11 Aug 2015 11:02:54 + Subject: Re: [Freesurfer] Permutation output Thanks. Sorry but I am not being able to figure it out yet. Basically I am not getting the expected outcome. So I thought to give you an idea of how I am running permutations. mri_glmfit-sim --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg And I am attaching a snapshot of the output files and the log of mdi_glmfit-sim. At this stage I am wondering whether in order to run permutation it is required use as input the output from fsgd rather than qdec, because my input is from qdec. Would this make any difference? Thanks. Pablo Date: Mon, 10 Aug 2015 11:13:13 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Permutation output It is the same thing, but the permutation output will have the name you gave the csdbase when you ran the simulation (ie, the 4th arg to --sim) On 08/10/2015 05:54 AM, pablo najt wrote: Thank you Doug. I run permutations with mdi_glmfit-sim --sim perm. Would you be able to advice on the output and how to open the permutation outputs? The tutorial instructs on how to open the *.summary file for the summary of clusters and *.sig.cluster.mgh the cluster corrected map, but not the permutation output. Thank you, Pablo Date: Fri, 7 Aug 2015 10:53:55 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec You can try permutation, though it is often more constraining than those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a question about running corrections for multiple comparisons. I am finding a fairly large cluster analyzing 2 groups on sulcal depth. However when I tried FDR or cluster wise correction the results do not seem to survive. As the result is on the region I was predicting I want to make sure there are no other options for correcting for multiple comparisons. I am including a figure of my result to give you an idea of the size of the cluster. Do you have any suggestions for trying alternative ways of correcting? Thank you in advance, Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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
Re: [Freesurfer] fcseed-sess problem
The problem is that you are using the wrong segmentation number for left insula. You used 19, which is reasonable given that FreeSurferColorLUT.txt lists that as left insula, but the one you want is actually 1035. doug On 08/12/2015 11:09 AM, Gay,Charles Wysaw wrote: Hi Doug - Here is some of the information: FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 - Please include the following additional information in your report: 1) subject name: B113v1 2) the entire command-line executed: [phhp-chazgay-mb:Bishop/FreeSurfer_R01/Project] chaz.gay% fcseed-sess -s B113v1 -cfg mean.L_Insula.config 3) the error message generated: see below - 4) optionally include the subject's /script/recon-all.log: attached. 5) SUBJECTS_DIR: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects Logfile is /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/log/fcseed-sess.L_Insula.dat.log.B113v1 Wed Aug 12 11:03:33 EDT 2015 Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess -s B113v1 -cfg mean.L_Insula.config freesurfer-Darwin-lion-stable-pub-v5.3.0 Wed Aug 12 11:03:33 EDT 2015 Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess -s B113v1 -cfg mean.L_Insula.config freesurfer-Darwin-lion-stable-pub-v5.3.0 mri_label2vol --seg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/B113v1/mri/aparc+aseg.mgz --reg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat --temp /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz --fillthresh .5 --o /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz --pvf /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz PVF /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz Outut Volume: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz Registration File: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -0.333 0.000 0.000 40.000; -0.000 -0.000 -0.333 40.000; -0.000 0.333 -0.000 19.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat RegMat: 1.000 -0.011 -0.001 9.758; -0.002 -0.246 0.969 -27.653; 0.011 0.969 0.246 -1.912; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -0.333 0.004 0.000 36.747; -0.004 -0.323 -0.082 40.637; -0.001 -0.082 0.323 9.782; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 234 (0 filled) ASeg2Vol: done PVF /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz Computing PVF 27 mri_binarize --i /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz --o /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz --match 19 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project cmdline mri_binarize --i
Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps
Those are more-or-less talairach coords, not MNI. If you add --nofixmni, the results will be reported in mni305 coords. On 08/10/2015 08:39 AM, Elijah Mak wrote: Hi Freesurfer Experts, For the purpose of defining nodes in a graph theory analysis, I would like to generate a list of X Y Z coordinates in MNI space for all the labels in the Destrieux atlas. I came across a previous post with the following steps: Step 1: mri_annotation2label --subject fsaverage --hemi lh --annotation aparc.a2009s --outdir /Users/ElijahMak Step 2: mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin --centroid --thmin 0 --hemi lh --subject fsaverage Everything went smoothly, but I would like to check my steps with you before I proceed to generate the coordinates individually for each ROI per hemisphere. The output from #2 issum.lh.G_and_S_frontomargin. When I load it, I see dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin # Cluster Growing Summary (mri_surfcluster) # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ # CreationTime 2015/08/10-12:29:31-GMT # cmdline mri_surfcluster --in /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin --centroid --thmin 0 --hemi lh --subject fsaverage # cwd /Users/ElijahMak # sysname Darwin # hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk http://dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # SUBJECTS_DIR /Applications/freesurfer/subjects # SearchSpace_mm2 65416.6 # SearchSpace_vtx 932 # Bonferroni 0 # Minimum Threshold 0 # Maximum Threshold infinity # Threshold Signabs # AdjustThreshWhenOneTail 1 # Area Threshold0 mm^2 # clabelfile lh.G_and_S_frontomargin.label # clabelinv 0 # Overall max 3.33248 at vertex 83949 # Overall min 0 at vertex 0 # NClusters 1 # Total Cortical Surface Area 65416.6 (mm^2) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs 13.332 83949 82219.39-29.4 -22.0 17.4 163842 Are those TalX TalY TalZ the values I'm looking for? Many thanks for your time. Best Wishes, Elijah -- Elijah Mak, PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] fcseed-sess problem
Hi Chaz, we'll need more info. Please see surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On 08/11/2015 11:40 PM, Gay,Charles Wysaw wrote: I've completed steps 1 thru 4 successfully (i think). When I run the fcseed-sess with the segid for the left insula I'm getting an segmentation fault. I've tried both segids 7 and 19 and have the same result. Selecting other seed regions (left posterior cingulate) generates a 1d file timecourse. the error log was the same both times: MRIalloc(0, 1, 1): bad parm Any ideas on what to do? Thanks Chaz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Creating proper FSGD file
On 08/12/2015 06:44 AM, Silas wrote: Hi Freesurfer team, I'm currently working on a functional group analysis using GLM (i've mapped my data onto the fsaverage). My problem is that I have more than one functional *.mgh file per subject, and i have troubles creating a proper FSGD file where i'm presenting each subject several times (btw i'm using mri_glmfit). 1) The solution to this problem might be to average (or sum) the *.mgh files of each subject and implement this average file in the FSGD. Which command is able to do this? Yes, use mri_concat file1.mgh file2.mgh --mean --o file12mean.mgh 2) Another solution to this problem is to present the subjects several times in the FSGD file or presenting several functional *.mgh files per subject in the FSGD file. Is this possible? This is also possible (it makes it a repeated measures design, which is more complicated. I would probably use #1 I've tried to use mris_preproc to concatenate the files and presenting the output files in mri_glmfit - but this does not seem to be the solution since mris_preproc only concatenates the files. Thank you for your help, Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 the outputs of recon-all
fsaverage is the surface-based common-space analogous to talairach for MNI space. This is the space where group analysis is done on the surface. You can run mris_preproc to get a stack of data in fsaverage space prior to running group analysis with mri_glmfit. See the on-line tutorials on the wiki. On 08/11/2015 09:46 PM, chenhf_uestc wrote: Dear Freesurfer experts, I am a new user of freesurfer and I just performed recon-all analyses. I have some questions about the pipeline (may be very simple ^_^). In the fMRI, I used SPM8 toolkit to perform preprocessing. After normalization, the images were transform to the MNI space. In the freesurfer, there are many folders in the output subject dir, e.g., bem, mri, script, surf. The first question, were the recon-all analyses performed in the individual spave (I mean, unlike spm or other software, there is no normalization procedure in freesurfer)? If in the individual space, we should transform all subjects' files into a common space for group-level analysis. How can I transform them? Did I transfrom these into MNI space or other space? In the fswiki, I have known that there is a fsaverage space. So, the second question is that what is the fsaverage space and what is the aim to introduce such space. Can I regard fsaverage space as a intermediate between individual space and MNI space? Further, in the recon-all analysis, there is a procedure of talairach transformation. Were the outputs transformed into talairach space? Any help will be greatly appreciately! Best, Feng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Registering surface files from fsaverage_sym to individual subjects
Those commands won't work, try something like this instead mris_apply_reg --src $s/xhemi/surf/xhemi.lh-rh.w-g.pct.mgh --trg $s/surf/rh.lh-rh.w-g.pct.mgh \ --streg $SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg $SUBJECTS_DIR/$s/surf/lh.fsaverage_sym.sphere.reg That may not be exactly the right command, but I can't tell you exactly because I don't know how xhemi.lh-rh.w-g.pct.mgh was created. If it is on the left hemi of fsaverage_sym, then it should be ok On 08/12/2015 05:18 AM, Adler, Sophie wrote: Hi All We have been using mris_surf2surf to register both left and right .mgh files to lh fsaverage_sym in order to compare surface files that are not automatically registered to xhemi/surf. We are having some trouble registering the rh files back to native space. This is what I have been trying: 1) mri_surf2surf --srcsubject fsaverage_sym --srcsurfval $s/xhemi/surf/xhemi.lh-rh.w-g.pct.mgh --trgsubject $s --trgsurfval $s/surf/rh.lh-rh.w-g.pct.mgh --hemi lh --srcsurfreg sphere.reg --trgsurfreg sphere.reg The output surface file values all equal 0. 2) mri_surf2surf --srcsubject fsaverage_sym --srcsurfval $s/xhemi/surf/xhemi.lh-rh.w-g.pct.mgh --trgsubject $s --trgsurfval $s/surf/rh.lh-rh.w-g.pct.mgh --hemi rh --srcsurfreg sphere.reg --trgsurfreg sphere.reg The output surface file is flipped - medial wall surface values on lateral wall and visa versa. Is there a way to register the files back from “$s”/xhemi/surf to “$s”/surf? Thanks, Sophie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] fcseed-sess problem
Hi Doug - Here is some of the information: FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 - Please include the following additional information in your report: 1) subject name: B113v1 2) the entire command-line executed: [phhp-chazgay-mb:Bishop/FreeSurfer_R01/Project] chaz.gay% fcseed-sess -s B113v1 -cfg mean.L_Insula.config 3) the error message generated: see below - 4) optionally include the subject's /script/recon-all.log: attached. 5) SUBJECTS_DIR: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects Logfile is /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/log/fcseed-sess.L_Insula.dat.log.B113v1 Wed Aug 12 11:03:33 EDT 2015 Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess -s B113v1 -cfg mean.L_Insula.config freesurfer-Darwin-lion-stable-pub-v5.3.0 Wed Aug 12 11:03:33 EDT 2015 Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess -s B113v1 -cfg mean.L_Insula.config freesurfer-Darwin-lion-stable-pub-v5.3.0 mri_label2vol --seg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/B113v1/mri/aparc+aseg.mgz --reg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat --temp /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz --fillthresh .5 --o /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz --pvf /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz PVF /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz Outut Volume: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz Registration File: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -0.333 0.000 0.000 40.000; -0.000 -0.000 -0.333 40.000; -0.000 0.333 -0.000 19.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat RegMat: 1.000 -0.011 -0.001 9.758; -0.002 -0.246 0.969 -27.653; 0.011 0.969 0.246 -1.912; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -0.333 0.004 0.000 36.747; -0.004 -0.323 -0.082 40.637; -0.001 -0.082 0.323 9.782; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 234 (0 filled) ASeg2Vol: done PVF /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz Computing PVF 27 mri_binarize --i /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz --o /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz --match 19 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project cmdline mri_binarize --i /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz --o /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz --match 19 sysname Darwin hostname phhp-chazgay-mb.ad.ufl.edu machine x86_64 user chaz.gay input
Re: [Freesurfer] FW: Permutation output
Will do that from now on. the output is as follow:This is the output I am getting which I believe is not what I need for check the permutation outputC.dat F.mgh cnr.mgh gamma.mgh gammavar.mghmaxvox.dat sig.mgh Date: Wed, 12 Aug 2015 11:17:38 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: Permutation output look in the folder of one of the contrasts (eg, rh-Diff-BD-HC-Intercept-sulc). Also, if you can paste such text into the email it is much more convenient for us than to sent us a tiff On 08/12/2015 11:12 AM, pablo najt wrote: Dear FS exp, In case my message got swamped, I am reposting my question. Many thanks! Pablo From: pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 11 Aug 2015 11:02:54 + Subject: Re: [Freesurfer] Permutation output Thanks. Sorry but I am not being able to figure it out yet. Basically I am not getting the expected outcome. So I thought to give you an idea of how I am running permutations. mri_glmfit-sim --glmdir rh_sulc_fwhm25 --sim perm 5000 1.3 perm.neg.13 --sim-sign neg And I am attaching a snapshot of the output files and the log of mdi_glmfit-sim. At this stage I am wondering whether in order to run permutation it is required use as input the output from fsgd rather than qdec, because my input is from qdec. Would this make any difference? Thanks. Pablo Date: Mon, 10 Aug 2015 11:13:13 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Permutation output It is the same thing, but the permutation output will have the name you gave the csdbase when you ran the simulation (ie, the 4th arg to --sim) On 08/10/2015 05:54 AM, pablo najt wrote: Thank you Doug. I run permutations with mdi_glmfit-sim --sim perm. Would you be able to advice on the output and how to open the permutation outputs? The tutorial instructs on how to open the *.summary file for the summary of clusters and *.sig.cluster.mgh the cluster corrected map, but not the permutation output. Thank you, Pablo Date: Fri, 7 Aug 2015 10:53:55 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Correction for multiple comparisons - qdec You can try permutation, though it is often more constraining than those other two options. To do this, you'll need to run mri_glmfit-sim from the command line using the --sim perm option. Run it with --help to get examples On 8/7/15 6:59 AM, pablo najt wrote: Dear FS experts, I have a question about running corrections for multiple comparisons. I am finding a fairly large cluster analyzing 2 groups on sulcal depth. However when I tried FDR or cluster wise correction the results do not seem to survive. As the result is on the region I was predicting I want to make sure there are no other options for correcting for multiple comparisons. I am including a figure of my result to give you an idea of the size of the cluster. Do you have any suggestions for trying alternative ways of correcting? Thank you in advance, Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing
Re: [Freesurfer] uploading a surface in freeview
Hi Carina the first argument after the -f has to be a surface file, not an overlay. For example try using lh.inflated or lh.pial cheers Bruce p.s. if you paste text into the emails instead of taking screen shots of text it would simplify things On Wed, 12 Aug 2015, car...@van-vlodrop.de wrote: Hi Bruce, I send you a screenshot of my command field with my command line and the following error message. Thank you very much for your help. Carina Gesendet: Dienstag, 11. August 2015 um 16:54 Uhr Von: Bruce Fischl fis...@nmr.mgh.harvard.edu An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] uploading a surface in freeview Hi Carina you need to send us your full command line and screen output otherwise we don't have enough information to help you. cheers Bruce On Tue, 11 Aug 2015, car...@van-vlodrop.de wrote: Hi Bruce, Thank you for your answer. When I type the path to the surface with the beginning and endling you told me, freeview opens with the error message 'failed to load surface' and in the command field it says 'MRISread failed'. Do you have any idea of how it is possible to avoid this error? Best regards, Carina Gesendet: Sonntag, 09. August 2015 um 16:33 Uhr Von: Bruce Fischl An: Freesurfer support list Betreff: Re: [Freesurfer] uploading a surface in freeview Hi Carina it should be something like: freeview -f /lh.inflated:overlay=mc-z.abs.2.sig.cluster.mgh assuming mc-z.abs.2.sig.cluster.mgh is in your current directory cheers Bruce On Sun, 9 Aug 2015, car...@van-vlodrop.de wrote: Hi Lilla, I still have the problem to display my surface created by the Monte Carlo analysis. There are several files generated and I think that 'mc-z.abs.2.sig.cluster.mgh' should be the correct one to show the overlay in freeview. Could you please tell me which complete command I have to type in after opening freesurfer? Thank you very much. Best regards, Carina Gesendet: Mittwoch, 16. Juli 2014 um 14:01 Uhr Von: Lilla Zollei An: Freesurfer support list Betreff: Re: [Freesurfer] uploading a surface in freeview Hi Carina, You can use the -f option (instead of -v used for volumes) when you are calling freeview from the commandline in order to display a surface and then append :overlay=overlay_filename after the filename to identify the overlay that you want to use. You will need to decide which hemi and which surface you want to use and type the full path to it and the same with the overlay. Lilla On Wed, 16 Jul 2014, car...@van-vlodrop.de wrote: Dear Freesurfer experts, I have already run a Monte Carlo Simulation and I would like to upload the results in freeview. The simulation created a file ending with .mgh and the tutorial identifies it to be the overlay. Do I have to upload a surface first and afterwards the overlay? How can I upload a surface and which is the right one? Yours sincerely, Carina ___ 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 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.
[Freesurfer] the effects of cortical edits
Hello Freesurfer Experts, Our group is trying to determine the importance of manual edits on our data. After discovering poor white matter segmentation in the supramarginal/inferiorparietal regions, we performed manual edits as described in the FsTutorial. Surprisingly, the areas we edited had relatively small changes on the aparc.stats table in rh.area (0-8%) and other regions we didn't edit, such as the bankssts, entorhinal, and parsopercularis regions had much larger changes in rh.area (11-20%). Does this mean that the edits (and presumably errors) in one region of the brain affect the entire cortical template? Thanks, -Eric ___ 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] FW: Freesurfer tool for children's data
Hi Lilla, Is the tool ready to be tested yet? Would be great to get it before SeptemberThank you! Best wishes, Kristina -Original Message- From: Mayer Kristina Sent: Monday, August 03, 2015 9:20 AM To: 'Freesurfer support list' Subject: RE: [Freesurfer] Freesurfer tool for children's data Hi Lilla, hoe is it going with the new stream? Is it ready to be tested? Would be great if you could send me the version soon, as I have now one month in research and plenty of time to try it!! Best wishes, Kristina -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei Sent: Friday, June 26, 2015 5:37 PM To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer tool for children's data Hi Kristina, I am working on a stream that will be applicable to exactly to this age group, but as Bruce mentioned it is not ready for prime time. I would prefer waiting another month or so before giving you a beta version. Would that work? Lilla On Thu, 25 Jun 2015, Mayer Kristina wrote: Hi Bruce, from 18-36 months of age. I got good results when adding some flags (adjustment of wsthresh, -bigventricles, -mprage) but still it is lot of work for adjustment, as the contrasts is slight different at that ageIs there a preliminary version I could try with? Would be great opportunity, as I also have data from fsl and wpm to compare with. Cheers, Kristina Von: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]quot; im Auftrag von quot;Bruce Fischl [fis...@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 24. Juni 2015 16:37 An: Freesurfer support list Betreff: Re: [Freesurfer] Freesurfer tool for children's data Hi Kristina what age? It works reasonably well down to 7 or even 5. Younger than that is something that Lilla Zollei has made a lot of progress on, but isn't ready for distribution yet cheers Bruce On Wed, 24 Jun 2015, Mayer Kristina wrote: Dear all, I was wondering if your free surfer pipeline (recon-all) is now available for children's data. If so, is there a page where it is described? Best wishes, Kristina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Creating proper FSGD file
Hi Freesurfer team, I'm currently working on a functional group analysis using GLM (i've mapped my data onto the fsaverage). My problem is that I have more than one functional *.mgh file per subject, and i have troubles creating a proper FSGD file where i'm presenting each subject several times (btw i'm using mri_glmfit). 1) The solution to this problem might be to average (or sum) the *.mgh files of each subject and implement this average file in the FSGD. Which command is able to do this?2) Another solution to this problem is to present the subjects several times in the FSGD file or presenting several functional *.mgh files per subject in the FSGD file. Is this possible? I've tried to use mris_preproc to concatenate the files and presenting the output files in mri_glmfit - but this does not seem to be the solution since mris_preproc only concatenates the files. Thank you for your help, Best, Silas ___ 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] Registering surface files from fsaverage_sym to individual subjects
Hi All We have been using mris_surf2surf to register both left and right .mgh files to lh fsaverage_sym in order to compare surface files that are not automatically registered to xhemi/surf. We are having some trouble registering the rh files back to native space. This is what I have been trying: 1) mri_surf2surf --srcsubject fsaverage_sym --srcsurfval $s/xhemi/surf/xhemi.lh-rh.w-g.pct.mgh --trgsubject $s --trgsurfval $s/surf/rh.lh-rh.w-g.pct.mgh --hemi lh --srcsurfreg sphere.reg --trgsurfreg sphere.reg The output surface file values all equal 0. 2) mri_surf2surf --srcsubject fsaverage_sym --srcsurfval $s/xhemi/surf/xhemi.lh-rh.w-g.pct.mgh --trgsubject $s --trgsurfval $s/surf/rh.lh-rh.w-g.pct.mgh --hemi rh --srcsurfreg sphere.reg --trgsurfreg sphere.reg The output surface file is flipped - medial wall surface values on lateral wall and visa versa. Is there a way to register the files back from “$s”/xhemi/surf to “$s”/surf? Thanks, Sophie ___ 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 Talairach
Hello, I was following the instructions on the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview to check the registrations on some subjects. I ran the following command from my subjects dir, to view subject 001: freeview -v 001/mri/T1.mgz 001/mri/brainmask.mgz:reg=001/mri/transforms/talairach.xfm I get the following errors: regio_read_mincxfm: No such file or directory ERROR: could not read /path/to/subjects_dir/001/mri/001/mri/transforms/talairach.xfm ERROR: could not read /path/to/subjects_dir/001/mri/001/mri/transforms/talairach.xfm Read registration failed The T1 file is loaded, but not the brainmask.mgz file. It looks like the command was expecting relative paths for the registration from the file, so I reran using: freeview -v 001/mri/T1.mgz 001/mri/brainmask.mgz:reg=transforms/talairach.xfm When I do that, it brings up both the T1 and brainmask file, but outputs a different error: Not reading in xfm fileinfo Not reading in xfm fileinfo The brainmask file appears shifted up and backwards considerably, but still centered widthwise. However, I am not sure if this has something to do with it not loading the file correctly, or if the transform was indeed erroneous. Appreciate any insight! Lauren Gresham Research Specialist Waisman Waisman Laboratory for Brain Imaging Behavior ___ 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] mris_register problem: No such file or directory
Hi, I've had time to come back to this problem. It was not solved after recreating the sphere. And plus, it happens in 30% of my subjects (Approximately). I have opened the sphere and I can see no problem there (nor there is any kind of error message after opening it. Could you tell me what files are used in the mris_register -curv command (appart from the obvious lh.sphere and lh.average.curvature.filled.buckner40.tif) in order to check if there is any problem with them. The fact that the original error message is No such file or directory is intriguing. Cheers. 2015-08-02 18:57 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: try opening it in tksurfer and see if it complains On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: Hi, Thanks for the quick answer. There was no error message in the previous steps. I started it with : mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere Although if the seed is the same, I am guessing that any non-deterministic process would have the same output. Is there a a way to automatically know if there was a problem in the sphere creation? Cheers. 2015-08-02 16:27 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: hmm, something seems to be wrong maybe the the ?h.sphere. Can you try recreating it cheers Bruce On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote: Hi all, I received an error in one of the steps of recon-all. The error is No such file or directory at the end of one of the registration processes. The step was mris_register -curv. The command was: mris_register -curv ../surf/lh.sphere FS_DIR/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg I already checked that ../surf/lh.sphere and FS_DIR/average/lh.average.curvature.filled.buckner40.tif exist (and are readable). I also checked that the output directorry (../surf/ ) has the proper permisons to write. The version of mris_register is stable5. Finally, the complete output message is (Please, note that the parts with have been edited by me for privacy reasons: # #@# Surf Reg lh Sun Aug 2 00:52:59 BST 2015 SUBJECT_DIR/scripts mris_register -curv ../surf/lh.sphere FS_DIR/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from FS_DIR/average/lh.average.curvature.filled.buckner40.tif... MRISregister() --- max_passes = 4 min_degrees = 0.50 max_degrees = 64.00 nangles = 8 tol=5.0e-01, sigma=0.0, host=HOST., nav=1024, nbrs=1, l_extern=1.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.00 nfields 0 scale 0.00 desired_rms_height -1.00 momentum 0.95 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris-nsize 1 mris-hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=HOST., nav=1024, nbrs=1, l_extern=1.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization 1 Reading lh.sulc curvature mean = -0.000, std = 0.575 curvature mean = 0.028, std = 0.935 curvature mean = -0.002, std = 0.850 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 32.00, -64.00) sse = 463438.8, tmin=0.7880 d=16.00 min @ (0.00, -4.00, 4.00) sse = 460445.8, tmin=2.3467 d=8.00 min @ (0.00, 0.00, -2.00) sse = 460199.6, tmin=3.1967 d=4.00 min @ (0.00, 0.00, 1.00) sse = 459864.8, tmin=4.0376 d=2.00 min @ (-0.50, -0.50,
Re: [Freesurfer] fcseed-sess problem
Thank you. issue resolved. On Wed, 12 Aug 2015 11:20:53 -0400, Douglas N Greve wrote: The problem is that you are using the wrong segmentation number for left insula. You used 19, which is reasonable given that FreeSurferColorLUT.txt lists that as left insula, but the one you want is actually 1035. doug On 08/12/2015 11:09 AM, Gay,Charles Wysaw wrote: Hi Doug - Here is some of the information: FREESURFER_HOME: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 14.0.0 x86_64 - Please include the following additional information in your report: 1) subject name: B113v1 2) the entire command-line executed: [phhp-chazgay-mb:Bishop/FreeSurfer_R01/Project] chaz.gay% fcseed-sess -s B113v1 -cfg mean.L_Insula.config 3) the error message generated: see below - 4) optionally include the subject's /script/recon-all.log: attached. 5) SUBJECTS_DIR: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects Logfile is /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/log/fcseed-sess.L_Insula.dat.log.B113v1 Wed Aug 12 11:03:33 EDT 2015 Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess -s B113v1 -cfg mean.L_Insula.config freesurfer-Darwin-lion-stable-pub-v5.3.0 Wed Aug 12 11:03:33 EDT 2015 Darwin phhp-chazgay-mb.ad.ufl.edu 14.0.0 Darwin Kernel Version 14.0.0: Fri Sep 19 00:26:44 PDT 2014; root:xnu-2782.1.97~2/RELEASE_X86_64 x86_64 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects cd /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/fsfast/bin/fcseed-sess -s B113v1 -cfg mean.L_Insula.config freesurfer-Darwin-lion-stable-pub-v5.3.0 mri_label2vol --seg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects/B113v1/mri/aparc+aseg.mgz --reg /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat --temp /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz --fillthresh .5 --o /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz --pvf /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz PVF /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz Number of labels: 0 Annot File: (null) Template Volume: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/template.nii.gz Outut Volume: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz Registration File: /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: (null) ProjTypeId: 0 ProjStart: 0 ProjStop: 0 ProjDelta: 0.1 Subject: (null) Hemi: (null) UseNewASeg2Vol: 1 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/freesurfer/subjects $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $ Template RAS-to-Vox: -0.333 0.000 0.000 40.000; -0.000 -0.000 -0.333 40.000; -0.000 0.333 -0.000 19.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 27 nHits Thresh: 13.5 Loading registration from /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/register.dof6.dat RegMat: 1.000 -0.011 -0.001 9.758; -0.002 -0.246 0.969 -27.653; 0.011 0.969 0.246 -1.912; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -0.333 0.004 0.000 36.747; -0.004 -0.323 -0.082 40.637; -0.001 -0.082 0.323 9.782; 0.000 0.000 0.000 1.000; ASeg2Vol: Building LUT ASeg2Vol: Sorting ASeg2Vol: Mapping ASeg2Vol: Reverse Map nmisses = 234 (0 filled) ASeg2Vol: done PVF /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/pvf.nii.gz Computing PVF 27 mri_binarize --i /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/seg.nii.gz --o /Volumes/projects/painimaging/Bishop/FreeSurfer_R01/Project/B113v1/rest/001/tmp.fcseed-sess.55576/mask.nii.gz --match 19 $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $
Re: [Freesurfer] options for 7T images...
We use a typical 3D-MPRAGE sequence, and we collect a PD image to remove the intensity inhomogeneities (http://www.ncbi.nlm.nih.gov/pubmed/19233292). Andrea On Mon, Aug 10, 2015 at 8:17 PM, Kyoko Fujimoto kyoncat@gmail.com wrote: Hi Andrea, Which sequence do you use at 7T? -Kyoko On Mon, Aug 10, 2015 at 4:23 AM, Andrea Grant gran0...@umn.edu wrote: I would be interested in details on a 7T stream also! Thank you, Andrea - Andrea Grant Visual Neuroimaging Technologist Center for Magnetic Resonance Research, University of Minnesota 2021 6th St. SE, Minneapolis, MN 55455, 612-626-4948 gran0...@umn.edu umn.edu/~gran0260 On Sun, Aug 9, 2015 at 9:33 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: sorry, had an old address for Kyoko On Sun, 9 Aug 2015, Bruce Fischl wrote: Hi Gonzalo Jon and Kyoko (both ccd) have put together a 7T stream, and should be able to help you out cheers Bruce On Sat, 8 Aug 2015, Gonzalo Rojas Costa wrote: Hi: Must I use any recon-all option for 7T images ?... Sincerely, Gonzalo Rojas Costa -- 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_volcluster
Hi there, Just following up. Any advice would be much appreciated! Thanks, Keji On Aug 10, 2015, at 1:50 PM, Morenikeji Adebayo k...@nmr.mgh.harvard.edu wrote: Hi there, The command I submitted is: mri_volcluster --in merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz --thmin 1.3 --minsizevox 5 --sign neg --sum adebayo_young_neut_p.05 —fsaverage How would I: 1) Specify the voxel size 2) Have the results output in MNI? Thanks, Keji On Aug 10, 2015, at 11:32 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 08/10/2015 10:47 AM, Morenikeji Adebayo wrote: Hi there, I have a a couple of question related to the output generated by the ‘mri_volcluster' command. 1) It seems that the command automatically assumes that my voxels are 8 mm^3. Is there a way to specify my voxel size when I run the command? It should use whatever the voxel size of the input is. Remember to include a command line. 2) The output is given in Talairach coordinates. Is there a way to specify the output in MNI coordinates? Can tell without your command line Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Recon-all output missing .mgh extension
Hello Pablo, Not all of the outputs end in .mgz. If you look at the recon-all dev table it will show you all of the steps recon-all takes and what the input/output are: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable Your output looks fine to me, but you can always check it against the table. Remember that this is the table for the developmental version, so it might not be identical to what your version of FS does. But you can always run recon-all with the -dontrun flag to get a list of all the commands. -Ani On 08/12/2015 07:30 AM, pablo najt wrote: Dear FS experts I recently came across the issue that my outputs from recon-all do not show .mgh extension. My original data was in analyse. I am aware of the potential problems but we unfortunately did not have nii or dicom available. Could this be the problem? I am attaching a screenshot with the output in the surf folder and a copy of the recon-all for one of the subjects. I would greatly appreciate your help on this. Pablo ___ 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] Regarding: Brainstem volumetric result
Hi Sampada, the two measurements are obtained through different methods. The aseg estimate is generally smaller because it doesn't include the whole midbrain, whereas the brainstem module does. Which one is more accurate depends on your anatomical definition of brainstem. Compared with the ASEG, the brainstem module has the advantage that it provides the parcellation into pons, medulla, midbrain and SCP. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Dr Sampada Sinha drsampadasi...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 12, 2015 3:52:36 PM Subject: [Freesurfer] Regarding: Brainstem volumetric result Dear freesurfer experts, I successfully managed to install and run the freesurfer dev version6 for brainstem segmentation analysis. But, looking at the result of brainstem volume in brainstemSsVolumes.v10.txt, the whole brainstem volume is 14439.355323 and the brainstem volume by recon-all out asegfile is 13217.8 in the same participant. Will you please let me know why this disparity is there? And which one is more accurate? We plan to use the medullary volume for our study (here the medullary volume of the participant is 3184.900208 ) Thanks and regards, Sampada -- Sampada Sinha AIIMS, New Delhi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_volcluster
It will produce results in the voxel size and space of merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz How was that file produced? What space is it in? On 08/10/2015 01:50 PM, Morenikeji Adebayo wrote: Hi there, The command I submitted is: mri_volcluster --in merged_encode_Young_NEUT_hit_V_miss_n41.nii.gz --thmin 1.3 --minsizevox 5 --sign neg --sum adebayo_young_neut_p.05 —fsaverage How would I: 1) Specify the voxel size 2) Have the results output in MNI? Thanks, Keji On Aug 10, 2015, at 11:32 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 08/10/2015 10:47 AM, Morenikeji Adebayo wrote: Hi there, I have a a couple of question related to the output generated by the ‘mri_volcluster' command. 1) It seems that the command automatically assumes that my voxels are 8 mm^3. Is there a way to specify my voxel size when I run the command? It should use whatever the voxel size of the input is. Remember to include a command line. 2) The output is given in Talairach coordinates. Is there a way to specify the output in MNI coordinates? Can tell without your command line Thanks, Keji --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu mailto:k...@nmr.mgh.harvard.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] ID-swapping freesurfer data?
On 08/10/2015 02:35 PM, Nate Vack wrote: On Fri, Aug 7, 2015 at 2:45 PM Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: On 08/07/2015 03:11 PM, Nate Vack wrote: Thanks. Any other file types I should look for tags in? I think the surfaces have the subject name imbedded in them. Would there be a way to take it out? I just looked, and they do not have the subject name in them. Out of curiosity, how do .mgz and nifti files differ? mgz files have a lot more header info Will converting to nifti and back strip important header info? yes Thanks! -Nate ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] Unpacking mosaic dicoms
Run sudo chmod a+rx /Applications/freesurfer/bin/mri_probedicom If it still does not work, then run ls -l /Applications/freesurfer/bin/mri_probedicom On 08/10/2015 01:32 PM, Eiran Vadim Harel wrote: Thanks Doug, I downloaded and rerun and changed the permissions but it still says: /Applications/freesurfer/bin/mri_probedicom: Permission denied. Any idea? Thanks, EIraqn On Monday, August 10, 2015 6:18 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Eiran, can you download the following two binaries and rerun? First make a backup copy of the ones that are there. Then copy the two below into $FREESURFER_HOME/bin (remove the .mac). ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.mac ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_probedicom.mac On 08/10/2015 08:31 AM, Eiran Vadim Harel wrote: Hello Freesurfers, I am using freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0. I tried unpacking mosaic functional dicoms taken with siemens prisma scanner using: dcmunpack -src /users/eiran/Desktop/BSMT/201_/Study20150415_184518_65000 -targ /Applications/freesurfer/BSMT_PROJECT/bsmt201 -run 11 bold nii f.nii -run 13 bold nii f.nii -run 14 bold nii f.nii -run 15 bold nii f.nii -run 16 bold nii f.nii -run 17 bold nii f.nii -run 18 bold nii f.nii -run 19 bold nii f.nii I get the following error message: WARNING: file /users/eiran/Desktop/BSMT/BSMT/201_JACOBY_TAMMY/Study20150415_184518_65000/20TA_Se11_fMRI_Open_Eyes/MR011001001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header The files were not anonymized nor changed. Any ideas how to deal with it? Thanks, Eiran ___ Freesurfer mailing list Freesurfer@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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Regarding: Brainstem volumetric result
Thankyou so much Eugenio! In that case I will go with the brainstem text file, since I am interested in measureing the medullary volume. Appreciate all your help! Kind regards, Sampada On Wed, Aug 12, 2015 at 9:58 AM, Eugenio Iglesias e.igles...@bcbl.eu wrote: Hi Sampada, the two measurements are obtained through different methods. The aseg estimate is generally smaller because it doesn't include the whole midbrain, whereas the brainstem module does. Which one is more accurate depends on your anatomical definition of brainstem. Compared with the ASEG, the brainstem module has the advantage that it provides the parcellation into pons, medulla, midbrain and SCP. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Dr Sampada Sinha drsampadasi...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 12, 2015 3:52:36 PM Subject: [Freesurfer] Regarding: Brainstem volumetric result Dear freesurfer experts, I successfully managed to install and run the freesurfer dev version6 for brainstem segmentation analysis. But, looking at the result of brainstem volume in brainstemSsVolumes.v10.txt, the whole brainstem volume is 14439.355323 and the brainstem volume by recon-all out asegfile is 13217.8 in the same participant. Will you please let me know why this disparity is there? And which one is more accurate? We plan to use the medullary volume for our study (here the medullary volume of the participant is 3184.900208 ) Thanks and regards, Sampada -- Sampada Sinha AIIMS, New Delhi ___ 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 -- Sampada Sinha AIIMS, New Delhi ___ 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] hello freesurfer developer~
HI expert ! My name is Areum. I have some question to you. 1. I was wondering about the stats.dat file in stats_table (in Qdec folder). Stats.dat file’s value mean that each area’s average (include whole vertex) or each area’s average (only significant vertex)? 2. Can I get whole vertex value or significant vertex value? Because, I want to compare two groups correlation using SPSS. In addition, I want to compare thickness, volume and surface area correlation within the one group using SPSS. 3. I currently use the default cluster size(significant area threshold is 0mm^2). So, I want to control cluster size larger than default cluster size. How can I control the cluster size? plz reply to me 2015-08-11 11:06 GMT+09:00 A-reum Min naniy...@gmail.com: HI expert ! My name is Areum. I have some question to you. 1. Does FreeSurfer offer a effect size? if that offer, how can i use effect size? 2. I was wondering about the stats.dat file in stats_table (in Qdec folder). Stats.dat file’s value mean that each area’s average (include whole vertex) or each area’s average (only significant vertex)? 3. Can I get whole vertex value or significant vertex value? Because, I want to compare two groups correlation using SPSS. In addition, I want to compare thickness, volume and surface area correlation within the one group using SPSS. 4. I currently use the default cluster size(significant area threshold is 0mm^2). So, I want to control cluster size larger than default cluster size. How can I control the cluster size? 5. In FreeSurfer manual, GLM and Qdec have a same results. But when I use the both(GLM, Qdec) group analysis program results are not same. What is differences between two analysis program? How can I get same result while GLM and Qdec? 6. How can I get surface area and volume using GLM(group analysis program)? plz reply to me 2015-08-10 21:35 GMT+09:00 A-reum Min naniy...@gmail.com: Hello developer~ I have some questions to you. 1. Does FreeSurfer offer a effect size? if that offer, how can i use effect size? 2. I was wondering about the stats.dat file in stats_table (in Qdec folder). Stats.dat file’s value mean that each area’s average (include whole vertex) or each area’s average (only significant vertex)? 3. Can I get whole vertex value or significant vertex value? Because, I want to compare two groups correlation using SPSS. In addition, I want to compare thickness, volume and surface area correlation within the one group using SPSS. 4. I currently use the default cluster size(significant area threshold is 0mm^2). So, I want to control cluster size larger than default cluster size. How can I control the cluster size? 5. In FreeSurfer manual, GLM and Qdec have a same results. But when I use the both(GLM, Qdec) group analysis program results are not same. What is differences between two analysis program? How can I get same result while GLM and Qdec? 6. How can I get surface area and volume using GLM(group analysis program)? thanks for your help 2015-07-27 14:28 GMT+09:00 A-reum Min naniy...@gmail.com: Hello bruce I solve this problem(12.png) Thank you 2015-07-27 13:03 GMT+09:00 dgw dgwake...@gmail.com: Hi A-reum, I think you may be able to get a faster response if you include some details about your setup: I would start with the following: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting and run bugr. hth D On 7/26/15 5:17 PM, A-reum Min wrote: Hi, Bruce When i use a Qdec, this message(12.png) show up.. How can i solve this problem? 2015-07-23 22:57 GMT+09:00 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu: 1. No, each subject has a different #. You can map to fsaverage (this is what -qcache does if you specify it for recon-all), then they will have the same #. 2. What result data do you mean? 3. Yes, although I'll leave the details to Doug (since I don't remember how his cluster code works). 4. The significance doesn't depend on the cluster size unless you do multiple comparison corrections (and even then only if you do them a certain way) cheers Bruce On Thu, 23 Jul 2015, A-reum Min wrote: HELLO developer I have some question to you.. 1. Every patient is given to the same number of vertex? 2. When i use a Qdec, How can I get the subject result data? 3. Could i get the significant vertex’s number, extent of the significant area and gray matter volume? 4. Is it significant blue color which how many connected vertex? 2015-05-29 2:03 GMT+09:00 A-reum Min naniy...@gmail.com mailto:naniy...@gmail.com: hello developer~ reconstruction is well done, so i'm doing on 'qdec' step..
[Freesurfer] Regarding: Brainstem volumetric result
Dear freesurfer experts, I successfully managed to install and run the freesurfer dev version6 for brainstem segmentation analysis. But, looking at the result of brainstem volume in brainstemSsVolumes.v10.txt, the whole brainstem volume is 14439.355323 and the brainstem volume by recon-all out asegfile is 13217.8 in the same participant. Will you please let me know why this disparity is there? And which one is more accurate? We plan to use the medullary volume for our study (here the medullary volume of the participant is 3184.900208 ) Thanks and regards, Sampada -- Sampada Sinha AIIMS, New Delhi ___ 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] Repost: Make liberal ROI masks
You'll need to merge the WM parcellation labels with those of their
matching GM parcellations. We do not have explicit software to do this.
You can do it in matlab, something like
a = MRIread('aparc.a2009s+aseg_liberal.mgz);
ind = find(a.vol == 3030); % 3030 = wm-lh-superiortemporal from
FreeSurferColorLUT.txt
a.vol(ind) = 1030; % 1030 = ctx-lh-superiortemporal
Do the rest of the parcellations in the same way, then
MRIwrite(a,'aparc.a2009s+aseg_liberal2.mgz');
On 08/10/2015 01:29 PM, Martin Hebart wrote:
Dear all,
In an earlier post, I was asking for help implementing dilated ROIs.
I was using Doug's suggestion
mri_aparc2aseg --subject 01 --a2009s --labelwm --wmparc-dmax 2 --o
aparc.a2009s+aseg_liberal.mgz
followed by
mri_label2vol --seg aparc.a2009s+aseg_liberal.mgz --regheader orig.mgz
--o rois.nii --temp sub.nii --subject 01
However, the written images are very similar to the original undilated
ROIs, so I guess this has to do with the fact that they labels within
white matter are still classified as white matter.
My question: How can I write the ROIs from the dilated labels?
Thanks!
Martin
P.S.: If this all is very difficult or impossible, I would be happy if
I could just write out a nifti for each label in the annotation file
which for each voxel reflects the probability of that label (i.e. not
binary masks, but probabilistic masks). Then I could do this process
manually.
2015-07-15 18:10 GMT+02:00 Martin Hebart martin.heb...@gmail.com
mailto:martin.heb...@gmail.com:
Dear Thomas and Doug,
Thanks a lot for your replies, I believe you fully answered my
question.
@Thomas: The reason I would like to dilate masks into white matter
is that although the masks are quite accurate for structural
volumes, the functional data doesn't perfectly fit the structural
(even when using a fieldmap). I don't want to miss any grey matter
voxels that might carry information, while including some white
matter is - for the purpose of my task - not detrimental.
Thanks again, I will try to implement Doug's suggestion!
Martin
2015-07-15 15:12 GMT+02:00 Thomas Yeo ytho...@csail.mit.edu
mailto:ytho...@csail.mit.edu:
Hi Martin,
I am a little confused. Can you explain a little more about
what you
need? Do you want the freesurfer cortical ROIs dilated into the
surrounding regions like white matter and CSF or something? If so,
then Doug's suggestion sounds reasonable.
In the case of my parcellation, I ran the MNI152 template through
recon-all, which unfortunately resulted in an overly conservative
estimate of gray matter (i.e., the tight mask in
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011).
Therefore I went through a rather complicated way of
generating the
liberal mask by registering the recon-all of 1000 subjects to MNI
space.
Since you appear to be working on an individual subject, the
freesurfer estimate of the cortical ROIs is likely to be quite
accurate. Why might you want to dilate them into CSF or white
matter?
Regards,
Thomas
On Wed, Jul 15, 2015 at 12:38 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
wrote:
There is not an easy way to do that, though Thomas might
want to chime
in. I would probably use the code that generates the wmparc
(mri_aparc2aseg --labelwm) to create labels in the adjacent
WM out to a
few mm (--wmparc-dmax 2), then merge the WM labels with the
GM labels
On 07/14/2015 08:18 AM, Martin Hebart wrote:
Dear Freesurfer users,
I would be really happy if someone could help me out on the
issue I
mentioned below.
What I want to do is create non-overlapping anatomical ROI
masks that
are not restricted to grey matter only.
Thanks a lot in advance!
Martin
-
Dear all,
I've created non-overlapping ROI masks using
mri_label2vol --seg aparc.a2009s+aseg.mgz --regheader
orig.mgz --o
rois.nii --temp sub.nii --subject 01
Now these ROI masks are actually quite conservative
concerning grey
matter vs. other structures, i.e. they are only on the grey
matter.
I've seen more liberal masks e.g. here:
https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011
I would like to create similarly liberal non-overlapping
ROI masks for
all ROIs in the voxel size defined by the image in --temp, but
Re: [Freesurfer] uploading a surface in freeview
Hi Bruce, I send you a screenshot of my command field with my command line and the following error message. Thank you very much for your help. Carina Gesendet:Dienstag, 11. August 2015 um 16:54 Uhr Von:Bruce Fischl fis...@nmr.mgh.harvard.edu An:Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff:Re: [Freesurfer] uploading a surface in freeview Hi Carina you need to send us your full command line and screen output otherwise we dont have enough information to help you. cheers Bruce On Tue, 11 Aug 2015, car...@van-vlodrop.de wrote: Hi Bruce, Thank you for your answer. When I type the path to the surface with the beginning and endling you told me, freeview opens with the error message failed to load surface and in the command field it says MRISread failed. Do you have any idea of how it is possible to avoid this error?Best regards, Carina Gesendet:Sonntag, 09. August 2015 um 16:33 Uhr Von:Bruce Fischl An:Freesurfer support list Betreff:Re: [Freesurfer] uploading a surface in freeview Hi Carina it should be something like: freeview -f /lh.inflated:overlay=mc-z.abs.2.sig.cluster.mgh assuming mc-z.abs.2.sig.cluster.mgh is in your current directory cheers Bruce On Sun, 9 Aug 2015, car...@van-vlodrop.de wrote: Hi Lilla, I still have the problem to display my surface created by the Monte Carlo analysis. There are several files generated and I think that mc-z.abs.2.sig.cluster.mgh should be the correct one to show the overlay in freeview. Could you please tell me which complete command I have to type in after opening freesurfer?Thank you very much. Best regards, CarinaGesendet:Mittwoch, 16. Juli 2014 um 14:01 Uhr Von:Lilla Zollei An:Freesurfer support list Betreff:Re: [Freesurfer] uploading a surface in freeview Hi Carina, You can use the -f option (instead of -v used for volumes) when you are calling freeview from the commandline in order to display a surface and then append :overlay=overlay_filename after the filename to identify the overlay that you want to use. You will need to decide which hemi and which surface you want to use and type the full path to it and the same with the overlay. Lilla On Wed, 16 Jul 2014, car...@van-vlodrop.de wrote: Dear Freesurfer experts, I have already run a Monte Carlo Simulation and I would like to upload the results in freeview. The simulation created a file ending with .mgh and the tutorial identifies it to be the overlay. Do I have to upload a surface first and afterwards the overlay? How can I upload a surface and which is the right one?Yours sincerely, Carina ___ 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 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
