Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

5.1 to 5.3
by Jonathan Holt 04 Dec '13

04 Dec '13

Hey guys, Moving a ton of data from v 5.1 to v 5.3, is there anything special that needs to be done with our 5.1 processed data to ensure consistency with data to be processed in 5.3? best, jon

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To believe non-convergence?
by Seán Froudist Walsh 04 Dec '13

04 Dec '13

Dear Jorge and FreeSurfers, I have just been running lme_mass_fit_vw for 6 hours, and I have seen many thousands of messages like the following: "Location 337813: Convergence at iteration 4. Initial and final likelihoods: 607.8828, 611.1052. Location 337812: Convergence at iteration 4. Initial and final likelihoods: 603.0934, 604.4513." etc.... There was the very occasional message saying the algorithm did not converge at some location, a message I saw only 2 or three times (although I wasn't looking at the matlab window for 6 hours straight, thankfully). I thought, so far, so good. I came in to work this morning however, and found that it had finished, with the following ugly message waiting for me: "Algorithm did not converge at 99.9997 percent of the total number of locations. Total elapsed time is 357.4368 minutes." I have two questions please. 1) Should I believe this message, even though it seems to contradict what has been printed to the screen while lme_mass_fit_vw was running? 2) If it really is a problem, what would you recommend I do to remedy it? Set the convergence epsilon to 10^5? Any help is much appreciated. Best wishes, Seán

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Re: [Freesurfer] [martinos-tech] FSFAST between-conditions contrasts
by Douglas N Greve 04 Dec '13

04 Dec '13

Hi Sue, that looks correct. I think it is an open question as to whether you should use the corrected maps or use the uncorrected and then correct the final map. Maybe someone else can chime in. doug On 10/23/2013 09:49 AM, Susan Ruiz wrote: > Hi Doug, > > This is /very/ helpful. > > Procedurally, would this be the correct approach? > > For positive % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.pos.sig.cluster.nii > condBvFix.th3.pos.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.pos.sig.cluster.nii --i > condBvFix.th3.pos.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o positive.AvsB.nii > > For negative % signal change from baseline clusters, use these files > resulting from mri_glmfit-sim: > condAvFix.th3.neg.sig.cluster.nii > condBvFix.th3.neg.sig.cluster.nii > condAvscondB.th3.pos.sig.cluster.niigrf.th3.pos.sig.cluster.nii > > then run: > % mri_concat --i condAvFix.th3.neg.sig.cluster.nii --i > condBvFix.th3.neg.sig.cluster.nii --i > condAvscondB.th3.pos.sig.cluster.nii --conjunct --o negative.AvsB.nii > > Note that for positive activation differences I would use sign=pos for > each condition vs fixation during mri_glmfit-sim, and for > "deactivation" clusters I use sign=neg for each condition vs fixation > during mri_glmfit-sim. BUT for both cases I use sign=pos for condition > A vs. condition B. > > Thanks so much! > > Best, > ~Sue > > > > On Tue, Oct 22, 2013 at 10:50 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Sue, I agree that they are not the same thing. There is not a > single > flag that will do what you want. What you are describing is a post-hoc > test. So you look for places where A != B, then within those > voxels you > do posthoc tests. You can implement this with a conjunction analysis > where you set up threeway conjunction A>B and A>0 and B>0. You can do > this with the --conjunt option to mri_concat > doug > > > On 10/21/2013 02:13 PM, Susan Ruiz wrote: > > Hi all, > > > > When running a functional analysis and comparing two experimental > > conditions, we observed that there are some voxels/vertices > where both > > condition A and condition B have a positive % signal change from > > baseline, and condition A has greater activity than condition B. > > > > In other regions, both condition A and condition B have negative % > > signal change from baseline, but condition B has a greater absolute > > value % signal change (thus relative to baseline condition B has > more > > "deactivation"--a term I am using since you all know what I mean > even > > if the term itself is imperfect). > > > > Since, in both cases, the % signal change is technically > condition A > > > condition B, the between-conditions maps do not distinguish > these two > > scenarios. FS-FAST sees these as being the same. Is there a way to > > tell FS-FAST to cluster these scenarios separately? Is there a > > compelling reason why I should not consider these different > > situations? It seems to me that the interpretation of what's taking > > place in these two scenarios is not identical. Agree or > disagree? Can > > FS-FAST distinguish these with a flag I don't know about? > > > > Thank you, > > ~Sue > > > > -- > > * * ** *** ***** ******** ************* > > Susan Mosher Ruiz, Ph.D. > > Research Scientist > > Boston University School of Medicine > > Laboratory of Neuropsychology > > VA Boston Healthcare System > > smosher(a)bu.edu <mailto:smosher@bu.edu> <mailto:smosher@bu.edu > <mailto:smosher@bu.edu>> > > * * ** *** ***** ******** ************* > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > 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. > > > > ------------------------------------ > > Yahoo! Groups Links > > <*> To visit your group on the web, go to: > http://groups.yahoo.com/group/martinos-tech/ > > <*> Your email settings: > Individual Email | Traditional > > <*> To change settings online go to: > http://groups.yahoo.com/group/martinos-tech/join > (Yahoo! ID required) > > <*> To change settings via email: > martinos-tech-digest(a)yahoogroups.com > <mailto:martinos-tech-digest@yahoogroups.com> > martinos-tech-fullfeatured(a)yahoogroups.com > <mailto:martinos-tech-fullfeatured@yahoogroups.com> > > <*> To unsubscribe from this group, send an email to: > martinos-tech-unsubscribe(a)yahoogroups.com > <mailto:martinos-tech-unsubscribe@yahoogroups.com> > > <*> Your use of Yahoo! Groups is subject to: > http://info.yahoo.com/legal/us/yahoo/utos/terms/ > > > > > -- > * * ** *** ***** ******** ************* > Susan Mosher Ruiz, Ph.D. > Research Scientist > Boston University School of Medicine > Laboratory of Neuropsychology > VA Boston Healthcare System > smosher(a)bu.edu <mailto:smosher@bu.edu> > * * ** *** ***** ******** ************* > __._,_.___ > Reply via web post > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJwa21mMTlwBF9TA…> > Reply to sender > <mailto:smosher@bu.edu?subject=Re%3A%20%5Bmartinos-tech%5D%20FSFAST%20between-conditions%20contrasts> > Reply to group > <mailto:martinos-tech@yahoogroups.com?subject=Re%3A%20%5Bmartinos-tech%5D%20FSFAST%20between-conditions%20contrasts> > Start a New Topic > <http://groups.yahoo.com/group/martinos-tech/post;_ylc=X3oDMTJlZjd2ZDVnBF9TA…> > Messages in this topic > <http://groups.yahoo.com/group/martinos-tech/message/5844;_ylc=X3oDMTM0a2Nkb…> > (3) > > Recent Activity: > > Visit Your Group > <http://groups.yahoo.com/group/martinos-tech;_ylc=X3oDMTJlcXY1cjhnBF9TAzk3Mz…> > > Yahoo! Groups > <http://groups.yahoo.com/;_ylc=X3oDMTJkdW8xcWpkBF9TAzk3NDc2NTkwBGdycElkAzQ5O…> > > Switch to: Text-Only > <mailto:martinos-tech-traditional@yahoogroups.com?subject=Change%20Delivery%20Format:%20Traditional>, > Daily Digest > <mailto:martinos-tech-digest@yahoogroups.com?subject=Email%20Delivery:%20Digest> > • Unsubscribe > <mailto:martinos-tech-unsubscribe@yahoogroups.com?subject=Unsubscribe> > • Terms of Use <http://info.yahoo.com/legal/us/yahoo/utos/terms/> • > Send us Feedback > <mailto:ygroupsnotifications@yahoogroups.com?subject=Feedback%20on%20the%20redesigned%20individual%20mail%20v1> > . > > __,_._,___ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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/

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can FSL read FS thickness files?
by Kaiming Yin 04 Dec '13

04 Dec '13

Dear FS guys, I have run the FS 5.3 and get thickness files e.g. lh.thickness and rh.thickness, could FSL read these? should we use files like nii instead of mgz, or is there some options for FSL to read mgz too? Thanks, Kaiming

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manual edits boundary 2 screenshots example for 3T adult
by Kaiming Yin 04 Dec '13

04 Dec '13

Dear guys, I have a simple question in the manual edits parts. I am using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 with Ubuntu 13.10, for a trial on a 3T adult data, and I attached the data 2 screenshot common examples here, personally I am not sure if the wm boundary seems good or not. So I hope if you can help have a look and see if this data has any place need edits. And also usually, for a 3T data like this, how many edits will be approximately needed? I mean will it usually cost several corrections enough? Or 10s? 30s? or even more? (sorry for the oversize of last email attachment) Great thanks, Kaiming

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Re: [Freesurfer] major lobes
by Mojdeh Zamyadi 04 Dec '13

04 Dec '13

Thanks Doug! maybe I'm making this too complicated! What I want is to know which label (number) corresponds to each of the main lobes. Right now my freeSurfer_lobes.nii.gz image has lables in the range of 0-100's (which is WM if not mistaken), and then labels in the range of 1000-1035 for the left and 2000-2035 for the right hemisphere with zero labels in 1002,1008-1035 & 2002,2008-2035! (and these labels correspond to the GM, correct?!) I tried --ctab option by running the following command: mri_annotation2label --subject P2 --hemi lh --ctab new_ColorTable.txt --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot but it's not saving anything! Could you please tell me how to properly use this option? Thanks again, -Mojdeh On 11/29/2013 04:28 PM, Douglas Greve wrote: > The commands look right and it sounds like you might have the right > result. What do you mean you are getting a detailed WM + GM > segmentation? If you just load freeSurfer_lobes.nii.gz into tkmedit, the > label names will be all messed up because you don't have the proper > color table, but you should still only get 7 per hemi. To get the proper > color table, run mri_annotation2label with --ctab, then merge the two > ctabs you get (lh and rh). You don't need to rerun mri_aparc2aseg > doug > > > > On 11/29/13 3:09 PM, Mojdeh Zamyadi wrote: >> Hi all, >> >> Since I haven't heard back about my question so far, I'm posting it >> again! Sorry about this but I really need your help! >> >> As mentioned in my previous posts, I'm interested in having the GM >> volumetric lobar masks (frontal, parietal, temporal, occipital, and >> insular) with the final goal of moving them the DTI space to perform >> thalamic parcellation. I've ran the following commands: >> >> 1- a. mri_annotation2label --subject P2 --hemi lh --lobesStrict >> freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot >> b. mri_annotation2label --subject P2 --hemi rh --lobesStrict >> freeSurfer_Results/P2/label/rh.freeSurfer_lobes.annot >> >> 2- mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o >> freeSurfer_Results/P2/label/freeSurfer_lobes.nii.gz >> >> I thought after doing this I'm going to get the 5 or 6 lobar labels, but >> instead I'm getting a detailed WM + GM segmentation. I looked at >> "FreeSurferColorLUT.txt" and tried to manually combine labels in the >> range of 1000-1035 for the left and 2000-2035 for the right hemisphere >> to get the lobe masks, but after having a closer look I realised that >> labels 1002,1008-1035& 2002,2008-2035 are all empty (ie. I only have 7 >> labels in each hemisphere)! so, I'm now not sure how to manually combine >> these labels either! >> >> Could someone PLEASE PLEASE clarify this for me! I would really >> appreciate any help! >> >> Thanks, >> -Mojdeh >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. >

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Re: [Freesurfer] R: Re: Linear regression
by Douglas N Greve 04 Dec '13

04 Dec '13

On 12/02/2013 03:14 PM, stdp82(a)virgilio.it wrote: > Tank you very much. > > A-Do you mean the partial correlation coeff (PCC) at each voxel > averaged over region? > Finally a linear regression is done between cortical thickness of a > composite region and NPS. However the authors discuss every individual > region as related to disease. So a table with partials correlations of > individuals ROIs with NPS seems useful to support the discussion. What did you do in the paper? The reviewer mentions a "composite region". Did you average the thickness over that region and then do the regression with NPS? > > B- I'd like to obtain the covariance matrix of the regression made > between cortical thickness, group and covariates. How can I do it? > I'm not sure what you mean. Would this be a different matrix for each > vertex? > I cite the referee: "The authors must provide the covariance matrix of > the regression made between cortical thickness, group and covariates > as supplementary information in order to increase the value of the > results." Sorry, I don't understand what the reviewer is asking for. doug > > I don't have Matlab for mri_glmfit_pcc matlab. > > Stefano > > > > > ----Messaggio originale---- > Da: greve(a)nmr.mgh.harvard.edu > Data: 2-dic-2013 20.47 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Linear regression > > > On 12/02/2013 02:22 PM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > I have some questions, please. > > > > I performed linear regression by qdec to find the regions where the > > cortical thinning correlates with neuropsychological test (NPS), > > taking in account 3 nuisance factors. > > > > A- I individuated some posterior regions and now I'd like to build a > > table with partials correlations of individuals ROIs with NPS. How can > > I obtain the values for each region? > Do you mean the partial correlation coeff (PCC) at each voxel averaged > over region? You can get PCC maps using the mri_glmfit_pcc matlab > command. You can then do the averaging over region using mri_segstats. > > > > B- I'd like to obtain the covariance matrix of the regression made > > between cortical thickness,group and covariates. How can I do it? > I'm not sure what you mean. Would this be a different matrix for each > vertex? > > > > C- Is there a specific reference for qdec? > No, it is just a GLM so any GLM reference will do. > > > > Thank you very much, > > > > > > Stefano > > > > > > > > > > > > _______________________________________________ > > 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 Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: 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(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: 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/

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talaraich.xfm and aseg.stats measurements
by Jonathan Harlap 04 Dec '13

04 Dec '13

I hope this question doesn't seem too dim, but hopefully someone can give me a simple answer… I'm currently interested in subcortical structure volumes, particularly hippocampus, so I'm looking in my subjects dirs at stats/aseg.stats to get those values. It's not clear to me if those measurements are in native or FS space and when I skim over the code for mri_segstats I don't see anything in there that applies a scaling factor to take into account the scale parameter of the native space to FS space transform, so I've been assuming that the volumes reported in aseg.stats are actually in FS space although that seems odd to me. So first off, are aseg.stats measurements in native or FS space? As a naive first attempt to calculate the scale factor myself I simply ran xfm2param on mri/transforms/talairach.xfm and then multiplied together all three scale factors to end up with something I could multiply the aseg.stats results by to get back to native space measurements. In one particular case I got a result of about 1.26. However, when I follow the directions at http://freesurfer.net/fswiki/FsAnat-to-NativeAnat to move the aseg.mgz into native space and then use mincstats to generate a histogram of the label values in the segmentation and compare that histogram to the same histogram generated from the FS space aseg.mgz, I find the values I get back from both files (a) don't match aseg.stats measurements and (b) are not scaled by anywhere close to 126% relative to each other. The former is undoubtedly a result of mri_segstats taking partial volume effects into account when calculating measurements, which is great, but the latter is genuinely surprising and makes me wonder if I'm making a bad assumption about what talairach.xfm is really supposed to represent. So - the real question of the day, how do I reliably get these subcortical volume measurements in native space using FreeSurfer? Cheers, Jonathan

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Re: [Freesurfer] gammavar.mgh?
by Kayle Sawyer 04 Dec '13

04 Dec '13

Hi Doug, Thanks for confirming how to calculate the 95% confidence interval of the slope for all my clusters. I realized that there was a small error in my formula, in that I should use the critical values from the t-distribution, not the z-distribution (so the SE multiplier will be more like 2.0 instead of 1.96, depending on my sample N). The problem is that mri_segstats trims the output at the 10,000ths place. Here is the cluster.summary and the segstats from the two clusters identified as significantly associated with age. mc-z.th1.3.neg.sig.cluster.summary: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -5.096 73213 4275.24 50.0 33.2 -7.2 0.00350 0.00280 0.00430 8455 parstriangularis 2 -3.802 51616 20825.27 4.9 -26.2 39.2 0.00010 0.00000 0.00020 41094 posteriorcingulate gamma.mgh: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 1 8455 8455.0 Seg0001 -0.0089 0.0027 -0.0147 -0.0038 0.0109 2 2 41094 41094.0 Seg0002 -0.0069 0.0017 -0.0132 -0.0023 0.0108 gammavar.mgh: # ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range 1 1 8455 8455.0 Seg0001 0.0000 0.0000 0.0000 0.0000 0.0000 2 2 41094 41094.0 Seg0002 0.0000 0.0000 0.0000 0.0000 0.0000 So, for the 95% CI of the slope for cluster #1, I would use these formulas (N=60, so the t-distribution 95% critical value is 2.0003): -0.0089+2.0003*sqrt(0.0000) -0.0089-2.0003*sqrt(0.0000) Is there any way to add more significant digits to the mri_segstats output? Thanks, -Kayle On Nov 4, 2013, at 6:31 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > Yes, that should work. > doug > > On 10/30/2013 03:35 PM, Kayle Sawyer wrote: >> Hi all, >> >> I would like to calculate the 95% confidence interval of the slope for a thickness cluster (vs age in years) produced by mri_glmfit-sim. >> >> I have obtained values for my clusters from gamma.mgh and gammavar.mgh using these two commands: >> >> mri_segstats --i gamma.mgh >> --seg mc-z.th1.3.neg.sig.ocn.mgh >> --excludeid 0 >> --sum mc-z.th1.3.neg.sig.ocn.gamma.segstats >> >> mri_segstats --i gammavar.mgh >> --seg mc-z.th1.3.neg.sig.ocn.mgh >> --excludeid 0 >> --sum mc-z.th1.3.neg.sig.ocn.gammavar.segstats >> >> Next, (for each cluster, within each segstats summary file) I would take the “mean” from gamma, and the “mean” from gammavar, and calculate the 95% CI thus: >> gamma + 1.96*sqrt(gammavar) >> gamma - 1.96*sqrt(gammavar) >> >> Would these two values would give me the 95% confidence interval for the effect of age on that cluster, in mm/year? >> >> Thanks, >> -Kayle >> >> ------------------------------------ >> >> Yahoo Groups Links >> >> <*> To visit your group on the web, go to: >> http://groups.yahoo.com/group/martinos-tech/ >> >> <*> Your email settings: >> Individual Email | Traditional >> >> <*> To change settings online go to: >> http://groups.yahoo.com/group/martinos-tech/join >> (Yahoo! ID required) >> >> <*> To change settings via email: >> martinos-tech-digest(a)yahoogroups.com >> martinos-tech-fullfeatured(a)yahoogroups.com >> >> <*> To unsubscribe from this group, send an email to: >> martinos-tech-unsubscribe(a)yahoogroups.com >> >> <*> Your use of Yahoo Groups is subject to: >> http://info.yahoo.com/legal/us/yahoo/utos/terms/ >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: 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/ > > > > 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. >

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FS v5.3.0 installation problem.
by Bondarenko M. 04 Dec '13

04 Dec '13

Dear Freesurfer support team, Thank you very much for such a good software. I don't use it but I know it from our users at Southampton University. I am trying to Install Freesurfer V 5.3.0 on our cluster in Southampton University but when I run a job on our cluster it always fails. I have checked all configurations files, I have looked to your manual many times but still can not figure out the problem. Could you please help me out with installation. Some information =- cat $FREESURFER_HOME/build-stamp.txt => freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 -- which mri_convert => /local/software/rh53/freesurfer/5.3.0/freesurfer/bin/mri_convert I have included my submitting bash script and also output file. Basically I am getting the error: " mghRead(/home/mb4/test/free/track2010FS/21655/mri/nu.mgz, -1): could not open file mri_em_register: could not open input volume nu.mgz. " I have also try to run "fixup_mni_paths" but it did not help. I have installed FS V4.0 and I did not have such a problem. Could you please have a look to my output and give me some advises. Thank you very much. Maksym Bondarenko _________________________ High Performance Computing iSolutions Building : 2 Office 5045 University of Southampton

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