Freesurfer November 2016

freesurfer@nmr.mgh.harvard.edu

120 participants
214 discussions

Re: [Freesurfer] mri_convert slope scale
by Rockers, Elijah D. 18 Nov '16

18 Nov '16

Doug, Can you verify? The dicom and mri_covnert .nii are identical (integer values, as per dicom convention) when we inspect the matrix in MATLAB. The img matrices for mri_convert and dcm2nii are also identical, the difference appears to be that dcm2nii retains the slope scale in the header, allowing the viewer (freeview, pmod, etc..) to apply it. We have been trying to nail down this issue for the last couple days, any insight would be appreciated. Eli On 11/09/2016 05:51 PM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 Date: Wed, 9 Nov 2016 16:01:18 -0500 From: Douglas N Greve > <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_convert > slope scale To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: > <908818ac-156f-f6d2-1338-694626cde58f(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed I think we > actually apply the scaling, so including it in the output would be > inappropriate. On 11/09/2016 03:03 PM, Rockers, Elijah D. wrote: >> >Hello, >> > >> >We have been using mri_convert to convert our dicoms into .nii niftis. >> >There is an entry in the .nii header for the slope scale, but >> >mri_convert appears to discard this value instead of copying it into the >> >header (whereas mricron retains this value) We prefer to use mri_convert. >> > >> >Is there a way to have mri_convert carry this value over? Why is it >> >being discarded? >> > >> >Thanks, >> >Eli >> > -- Elijah Rockers Research Data Analyst Houston Methodist Research Institute O: 713-363-7729 Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Re: [Freesurfer] Comparing z score maps between 2 modalities in a group?
by Elijah Mak 18 Nov '16

18 Nov '16

Hi Doug, Thanks for taking a look at the commands! I would like to ask a further question about your concern/s regarding this approach? My aim was to have an analytical pipeline in Freesurfer that is analogous to several studies (using VBM-type of analyses in SPM) where they compared the relative severity of various pathological processes measured from different modalities. I have attached a little screenshot for your reference. For example, the authors in that study were trying to see whether hypometabolism was relatively more severe compared to atrophy, and both modalites (PET and T1) were Z-scored relative to controls, and then compared against each other. Another study that has used a similar technique is here: https://www.ncbi.nlm.nih.gov/pubmed/24951642 Best Wishes, Elijah Re: [Freesurfer] Comparing z score maps between 2 modalities in a group? <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subje…> Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Fri, 18 Nov 2016 08:19:47 -0800 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Those commands look right, though I would do the smoothing before computing the standard dev. Also, I don't know whether your overall method is valid. On 11/15/2016 05:48 PM, Elijah Mak wrote: > Hi Freesurfer Team, > > We would like to compare Z-scored surface maps between different > modalities (MRI and PET) within a single group. 1 subject = 2 measures. > > These are my steps so far, using mri_concat and fscalc for the > generation of the Z score maps. Differences between Z-score maps are > tested using the paired t-test approach as outlined here: > https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis > > I am not sure if my following steps are correct, so confirmation will > be much appreciated, many thanks for your time and help! > > // Generate mean/sd of healthy controls > > X > mri_concat --f stacks_X_lh_HC_fsaverage --o group_mean_X_hc_lh.mgh --mean > mri_concat --f stacks_X_lh_HC_fsaverage --o group_std_X_hc_lh.mgh --std > > Y > mri_concat --f stacks__Y_HC_fsaverage --o group_mean_Y_HC_lh.mgh --mean > mri_concat --f stacks_Y_lh_HC_fsaverage --o group_std_Y_HC_lh.mgh --std > > QN: Should smoothing be applied here or before? > > // Derive individual Z-score map for X and Y > > X > for i in `cat list`; do fscalc $i/surf/lh.X.fsaverage.mgh sub > group_mean_X_hc_lh.mgh div group_std_X_hc_lh.mgh --o > $i/surf/lh.Z.thickness.fsaverage.mgh; done > for i in `cat list; do fscalc $i/surf/rh.X.fsaverage.mgh sub > group_mean_cth_hc_rh.mgh div group_std_X_hc_rh.mgh --o > $i/surf/rh.Z.thickness.fsaverage.mgh; done > > Y > for i in `cat list`; do fscalc $i/surf/lh.Y.fsaverage.mgh sub > group_mean_X_hc_lh.mgh div group_std_cth_hc_lh.mgh --o > $i/surf/lh.Z.fsaverage.mgh; done > for i in `cat list; do fscalc $i/surf/rh.Y.fsaverage.mgh sub > group_mean_Y_hc_rh.mgh div group_std_Y_hc_rh.mgh --o > $i/surf/rh.Z.fsaverage.mgh; done > > > // Derive paired-difference of Z scores between X and Y > > mri_concat --f stacks_XminusY_lh --paired-diff --o concat_XminusY_lh.mgh > mri_concat --f stacks_XminusY_rh --paired-diff --o concat_XminusY_rh.mgh > > // Smooth concatenated maps of paired differences > > mri_surf2surf --s fsaverage --hemi lh --fwhm 4 --sval > concat_XminusY_lh.mgh --tval concat_XminusY_lh_sm4.mgh > > // Test significance of paired differences within the group > > mri_glmfit --y concat_XminusY_lh_sm4.mgh --fsgd fsgd_pairediff dods > --osgm --surf fsaverage lh --cortex --glmdir > > I used the --osgm flag as there are no covariates here. > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)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/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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.

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Correcting for multiple comparisons using clustering and external data
by ERIK JAHNER 18 Nov '16

18 Nov '16

Dear free surfer experts, I was wondering if someone could give me some general guidance on controlling for multiple comparisons using clustering and FDR. This the situation. I completed an analysis of functional data by first dividing the cortex into parcellations using the icosahedron 5 file then exported the values to matlab. I now have a correlation and significance value for all 10242 parcelations. My uncorrected results made theoretical sense, topologically. However, I attempted to use an FDR procedure on all these parcellations setting the FDR at .05 and no parcellations remained (all values were above the .05 threshold). Because my parcelationas are likely topologically correlated with the nearest neighboring clusters, it is my understanding that it makes more sense to use a clustering method to first identify clusters and then run a correction using FDR as cited in Chumbley, & Friston 2009. To complete clustering prior to FDR, I have projected the significance values from the parcellations back onto the surface vertices and then run the clustering approach described in the group analysis tutorial (mri_glmfit.sim). I have projected these group results onto the associated vertices on the fsaverage5 surface. However, when I run mri_glmfit.sim, no clusters remain. I believe that I am running into this problem because I am trying to get clusters of vertices when the data was actually analyzed using 10242 ROIs. Please note, I have placed the correlation and significance values (from my analysis in matlab) in a slope directory under GLM prior to running the analysis on the significance values associated with each vertex. By replacing the significance file generated from a thickness study with the significance file that I created, does freesurfer conduct the same analysis without reference to the type of data; does it only matter that I am using significance values or should I be replacing another file in the directory (I am using a different methodology to obtain my correlation and significance values)? The fsgd file that is in the folder still represents the groups correctly even though the neural data has been changed external to free surfer. Any suggestions or appropriate literature on how to correct for multiple comparisons using clusters of ROIs on surface would be appreciated? Thank you, Erik Jahner

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Re: [Freesurfer] Extracting structural measures from trend-level PET clusters
by Elijah Mak 18 Nov '16

18 Nov '16

Hi Doug, I am not sure if this is the correct way to reply to the thread. I thought that adding a "RE:" in front of the subject would automatically link the email to its orginal thread. I hope this works! I am pasting the previous emails below. Thanks again, Doug. Re: [Freesurfer] Extracting structural measures from trend-level PET clusters <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subje…> Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Mon, 14 Nov 2016 08:07:03 -0800 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Hi Elijah, can you repost with previous correspondence included? We get a lot of emails here and can't keep track of each person's issue. thanks! doug On 11/11/2016 08:06 PM, Elijah Mak wrote: > Hi, > > A bit more info: the stack of thickness maps consists of > lh.thickness.fwhm15.fsaverage.mghs that were created after -qcache. I > used mri_concat --f --o to create the stack of mghs. I also noticed > that the vertex values are in the range of 20-30, whereas those in the > lh.thickness.fsvaerage mghs are in the expected range. > > Should I be using this for the calculation of the thickness in the > clusters instead? > > Best Wishes, > Elijah > > On Sat, Nov 12, 2016 at 12:15 AM, Elijah Mak <fk...(a)medschl.cam.ac.uk > <mailto:fk...@medschl.cam.ac.uk <fk...(a)medschl.cam.ac.uk>>> wrote: > > Thanks, Doug. > > It works but I am not sure if the values I'm getting are correct. > Is this supposed to be reporting the mean cortical thickness of > each cluster? I have pasted the output below from the avgwf > below. The names of the clusters correspond to the regions from > the "summary" text, am I right? > > > Group lh_fusiform lh_precentral lh_insular lh_precuneus > lh_parsorbitalis > 1 24.29454 29.53935 14.24736 28.97924 > 31.54577 > 1 25.68872 28.26156 17.47828 28.20604 > 30.38902 > 2 25.46281 30.75879 19.34943 29.59019 > 32.0404 > 2 25.55514 27.23871 17.27937 29.14274 > 29.75657 > > > Another related question: Is it possible to simply take the mean > cortical thickness across the voxels exceeding p<0.001 from the > uncorrected sig.mgh? > > Thanks again! > > Best Wishes, > Elijah > > > > > -- > > Elijah Mak, Gates Scholar > > PhD Candidate *|* Psychiatry > > University of Cambridge > > Trinity College, Cambridge, CB2 1TQ > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Centergr...(a)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/filedrop2www.nmr.mgh.harvard.edu/facility/… Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ *Re: [Freesurfer] Extracting structural measures from trend-level PET clusters* <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subje…> Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Wed, 09 Nov 2016 13:22:06 -0800 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> You can just mri_segstats --i thickness.stack.mgh --seg cache.th30.pos.sig.ocn.nii.gz --excludeid 0 --avgwf thickness.stack.cluster.dat Each row in thickness.stack.cluster.dat will be a subject, and each column is a cluster On 11/09/2016 04:16 PM, Elijah Mak wrote: > Hi Freesurfer Team, > > 1) We've found some subtle differences in tau accumulation between two > groups. Unfortunately, it does not survive mri_glmfit-sim (voxel > threshold 0.001, cwp < 0.05). Still, I would like to extract the > structural measures from the uncorrected tau clusters (p<0.001). What > is the most convenient approach for this? > > Could the following URL > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16268.html > <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16268.html> > ) be a solution? Can mri_label2label work for sig.mgh with multiple > clusters? > > 2) A slightly unrelated question: how can I go about using this > particular cluster as a seed for functional or tractography analysis > in other softwares (i.e. FSL or MRTRIX) or even within Freesurfer if > possible? > > Thanks again. Really appreciate your help

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Comparing z score maps between 2 modalities in a group?
by Elijah Mak 18 Nov '16

18 Nov '16

Hi Freesurfer Team, We would like to compare Z-scored surface maps between different modalities (MRI and PET) within a single group. 1 subject = 2 measures. These are my steps so far, using mri_concat and fscalc for the generation of the Z score maps. Differences between Z-score maps are tested using the paired t-test approach as outlined here: https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis I am not sure if my following steps are correct, so confirmation will be much appreciated, many thanks for your time and help! // Generate mean/sd of healthy controls X mri_concat --f stacks_X_lh_HC_fsaverage --o group_mean_X_hc_lh.mgh --mean mri_concat --f stacks_X_lh_HC_fsaverage --o group_std_X_hc_lh.mgh --std Y mri_concat --f stacks__Y_HC_fsaverage --o group_mean_Y_HC_lh.mgh --mean mri_concat --f stacks_Y_lh_HC_fsaverage --o group_std_Y_HC_lh.mgh --std QN: Should smoothing be applied here or before? // Derive individual Z-score map for X and Y X for i in `cat list`; do fscalc $i/surf/lh.X.fsaverage.mgh sub group_mean_X_hc_lh.mgh div group_std_X_hc_lh.mgh --o $i/surf/lh.Z.thickness.fsaverage.mgh; done for i in `cat list; do fscalc $i/surf/rh.X.fsaverage.mgh sub group_mean_cth_hc_rh.mgh div group_std_X_hc_rh.mgh --o $i/surf/rh.Z.thickness.fsaverage.mgh; done Y for i in `cat list`; do fscalc $i/surf/lh.Y.fsaverage.mgh sub group_mean_X_hc_lh.mgh div group_std_cth_hc_lh.mgh --o $i/surf/lh.Z.fsaverage.mgh; done for i in `cat list; do fscalc $i/surf/rh.Y.fsaverage.mgh sub group_mean_Y_hc_rh.mgh div group_std_Y_hc_rh.mgh --o $i/surf/rh.Z.fsaverage.mgh; done // Derive paired-difference of Z scores between X and Y mri_concat --f stacks_XminusY_lh --paired-diff --o concat_XminusY_lh.mgh mri_concat --f stacks_XminusY_rh --paired-diff --o concat_XminusY_rh.mgh // Smooth concatenated maps of paired differences mri_surf2surf --s fsaverage --hemi lh --fwhm 4 --sval concat_XminusY_lh.mgh --tval concat_XminusY_lh_sm4.mgh // Test significance of paired differences within the group mri_glmfit --y concat_XminusY_lh_sm4.mgh --fsgd fsgd_pairediff dods --osgm --surf fsaverage lh --cortex --glmdir I used the --osgm flag as there are no covariates here.

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Recon-all: stochastic mri_nu_correct error when run on HPC cluster
by Anders Perrone 18 Nov '16

18 Nov '16

Hi FreeSurfer Developers, I'm running freesurfer from the HCP pipeline developed by the Washington University in St. Louis. It ran just fine on our university's cluster, but when I migrated the pipeline to Exacloud, Intel's HPC cluster, the recon-all command began randomly failing. Occasionally it will work on the first try, but more often than not the same command has to be re-run upwards of 30 times before it will succeed. I've provided the recon-all command and the relevant section of the log file including the error here (attached is the full recon-all.log file): recon-all -i ./T1w/T1w_acpc_dc_restore_1mm.nii.gz -subjid ${SUBJECT_ID} -sd . /T1w -motioncor -tal airach -nuintensitycor -normalization ... [perronea(a)exanode-3-9.local${PWD}/T1w/washu_INV0WC5U4JA/mri/] [2016-11-17 13:08:38] running: /home/exacloud/lustre1/users/mirandad/usr/local/freesurfer53/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.223851/nu1.mnc ./tmp.mri_nu_correct.mni.223851/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:.........................................................................................................................................................mincresample: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. nu_evaluate: crashed while running mincresample (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct Linux exanode-3-9.local 2.6.32-504.30.3.el6.x86_64 #1 SMP Wed Jul 15 10:13:09 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s washu_INV0WC5U4JA exited with ERRORS at Thu Nov 17 13:08:40 PST 2016 It doesn't appear than any similar errors have been reported on freesurfer. Our current work-around is to simply re-run the job on different nodes until it works, but this is not a sustainable long-term solution. Any guidance on troubleshooting this error would be greatly appreciated. FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Platform: CentOS release 6.5 (FINAL) uname -a: Linux exalab3.ohsu.edu 2.6.32-504.12.2.el6.x86_64 #1 SMP Wed Mar 11 22:03:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux Thanks, Anders Anders Perrone, Research Assistant I Fair Neuroimaging Lab perronea(a)ohsu.edu<mailto:perronea@ohsu.edu> 503-418-1897 Oregon Health & Science University Mail code:L470 3181 SW Sam Jackson Park Road Portland, Oregon 97239-3098 [cid:image001.png@01D240D7.C6F2C170] "If there is no solution to the problem then don't waste time worrying about it. If there is a solution to the problem then don't waste time worrying about it." - Dalai Lama XIV

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Version 6 Beta on Virtual Box problem
by Jeffrey Crawford 18 Nov '16

18 Nov '16

Hello everyone! I am currently using Virtual Box to run Freesurfer and I was wondering if my plan to put the version 6 beta on to my current virtual box was a valid one. My plan was to delete the Freesurfer folder off of the 5.3 virtual box and replace it with the Freesurfer version 6 folder. However, the virtual box is not letting me delete the Freesurfer folder. So I have some questions: 1. Does anyone have an idea of how I would go about deleting the original Freesurfer folder, so I could continue with this plan? 2. Is this plan a good one? 3. Should I try and download another linux virtual box somewhere and put the version 6 beta on that?

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Re: [Freesurfer] v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
by Antonin Skoch 18 Nov '16

18 Nov '16

Dear Bruce, see the screenshot in the attachment. The coords (RAS) are: 2.2 -23.3 35.9. The subject I have uploaded has this issue on multiple spots. The issue is quite frequent, I have seen similar spots in several other subjects I have checked so far. Antonin ------------------------------------------- Hi Antonin I'm having trouble parsing your image. Could you:1. Send the voxel coords of the location that you see overlap. 2. Send an image with *only* the two overlapping surfaces on, shown in different colors? thanks Bruce On Fri, 18 Nov 2016, Antonin Skoch wrote: Dear FreeSurfer experts, I am using HCP pipelines with my custom modifications of FreeSurferHiResWhite.sh (especially to accomodate full-hires reconstruction) to generate white and pial surfaces. I tested the v6.0 beta mris_make_surfaces binary to hopefully fix some problems with surfaces I found previously with 5.3.0_HCP version. This update helped to fix my problems but I found that with v.6.0 there is a new issue with overlaping pial surfaces in hemispherical region. This issue is not present in 5.3.0 version of mris_make_surfaces. My command line is mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled filled.hires -wm wm.hires -mgz -sdir my_subject_dir -orig white.deformed -nowhite -orig_white white.deformed -orig_pial pial -T2 my_subj/mri/T2w_hires.norm -T1 T1w_hires_norm my_subject_id lh The previous invocation of mris_make_surfaces in FreeSurferHiResWhite.sh (which does not use T2 refinement): mris_make_surfaces -variablesigma 4 -white NOWRITE -aseg aseg.hires -orig white.deformed -filled filled.hires -wm wm.hires -sdir my_subject_dir -mgz -T1 T1w_hires_norm my_subject_id lh produces surfaces which do not overlap. It seems to me that -aseg option of mris_make_surfaces (preventing surfaces to crossing the midline) is not active in case of -T2 refinement. I also tried to add -white NOWRITE or -cover_seg parameters, but it did not helped either. See attached screenshot aseg.hires overlaid with surfaces: blue are surfaces without T2 refinement (without interhemispheric overlap), yellow are surfaces after T2 refinement (with interhemispheric overlap). Attached is also the log file of my mris_make_surfaces -T2 command. I also uploaded the subject overlapping_surfs.tar.gz to your FTP file exchange server. Regards, Antonin Skoch

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v6.0_beta - mris_make_surfaces -T2 refinement -issue with overlapping pial surfaces
by Antonin Skoch 18 Nov '16

18 Nov '16

Dear FreeSurfer experts, I am using HCP pipelines with my custom modifications of FreeSurferHiResWhite.sh (especially to accomodate full-hires reconstruction) to generate white and pial surfaces. I tested the v6.0 beta mris_make_surfaces binary to hopefully fix some problems with surfaces I found previously with 5.3.0_HCP version. This update helped to fix my problems but I found that with v.6.0 there is a new issue with overlaping pial surfaces in hemispherical region. This issue is not present in 5.3.0 version of mris_make_surfaces. My command line is mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled filled.hires -wm wm.hires -mgz -sdir my_subject_dir -orig white.deformed -nowhite -orig_white white.deformed -orig_pial pial -T2 my_subj/mri/T2w_hires.norm -T1 T1w_hires_norm my_subject_id lh The previous invocation of mris_make_surfaces in FreeSurferHiResWhite.sh (which does not use T2 refinement): mris_make_surfaces -variablesigma 4 -white NOWRITE -aseg aseg.hires -orig white.deformed -filled filled.hires -wm wm.hires -sdir my_subject_dir -mgz -T1 T1w_hires_norm my_subject_id lh produces surfaces which do not overlap. It seems to me that -aseg option of mris_make_surfaces (preventing surfaces to crossing the midline) is not active in case of -T2 refinement. I also tried to add -white NOWRITE or -cover_seg parameters, but it did not helped either. See attached screenshot aseg.hires overlaid with surfaces: blue are surfaces without T2 refinement (without interhemispheric overlap), yellow are surfaces after T2 refinement (with interhemispheric overlap). Attached is also the log file of my mris_make_surfaces -T2 command. I also uploaded the subject overlapping_surfs.tar.gz to your FTP file exchange server. Regards, Antonin Skoch

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differences between OS recon all output, longitudinal data
by anonymous anonymous 18 Nov '16

18 Nov '16

Hi I am using recon-all in some longitudinal data on a ubuntu 16.04, and using the development version of freesurfer as I was told here, because the other current version doesnt work on ubuntu 16.04. The problem is that the first scans were probablly processed using virtualbox in a windows and an older version of freesurfer. i think I already know the answer, that I can't do this if I dont want to bias my results. Can I? But I'm using a better computer now and I use the one with windows for other analyses, so I wanted to know if I could install Virtual box on my ubuntu 16.04 computer, and install the same version of linux used to process the first measure. Should I also need to use the same version of freesurfer? f the computer's specs are dfferent, does it matter? And if I assign different cpu and ram on my virtual machine? Thank you!

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Freesurfer November 2016