Hi, I have a question running fsfast in my Mac, The mkcontrast command gave the error of can not launch matlab. Could you please let me know how to solve this problem. Thank you very much
Yongxia On Wednesday, May 22, 2013, wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. recon-all error (Yizhou Ma) > 2. Re: Still confused by group analysis.. (Tudor Popescu) > 3. Re: ERROR in long_mris_slope (Martin Reuter) > 4. Re: ERROR in long_mris_slope (Martin Reuter) > 5. temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma) > 6. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Chris Watson) > 7. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma) > 8. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Bruce Fischl) > 9. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma) > 10. Re: temporal lobe left out in pial surface - edits on > brainmask.mgz or brain.finalsurfs.mgz? (Yizhou Ma) > 11. Re: ERROR: recon-all -subcortseg (Akio Yamamoto) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 May 2013 13:19:35 -0400 > From: Yizhou Ma <ym...@nyu.edu> > Subject: [Freesurfer] recon-all error > To: freesurfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > cahqjiv6t-fkqrwcffg8r5o9gjrtzste+zgku0qvd2j7aons...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear FS experts, > > I have a recon-all error regarding one of my subjects. The scan suffers > from weakened signals at the lower part of the brain. Skullstrip stripped > most of the cerebellum at first, and we fixed it manually. After running > recon-all for the first time, large portions of the temporal lobes were > left out of the brain. Knowing that this may not be the correct way, we > still tried to fixed that by adding lots of control points. The second run > of recon-all, then, came back with the following error message:" > > Loading source data > Reading curvature file > /space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness > ERROR: number of vertices in > /space/mdeh3/3/halgdev/projects/nyuproj/subjects/sub4422b/surf/rh.thickness > does not match surface (192226,134773) > ERROR: reading curvature file > Linux mmil-compute-1-11.local 2.6.18-308.16.1.el5 #1 SMP Tue Oct 2 22:01:43 > EDT 2012 x86_64 x86_64 x86_64 GNU/Linux > recon-all -s sub4422b exited with ERRORS at Mon May 20 > " > > Any ideas for why it is, or how we can fix the problem at the temporal > lobes, will be really appreciated. > > Thanks, > Cherry > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130522/658d7f38/attachment-0001.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: sub4422b_125.png > Type: image/png > Size: 37879 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130522/658d7f38/attachment-0002.png > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: sub4422b_135.png > Type: image/png > Size: 38974 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130522/658d7f38/attachment-0003.png > > ------------------------------ > > Message: 2 > Date: Wed, 22 May 2013 18:43:33 +0100 > From: Tudor Popescu <tud...@gmail.com> > Subject: Re: [Freesurfer] Still confused by group analysis.. > To: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Cc: free surfer <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CAGBir427LRNUP1ff3CEgstVq0B= > dtrzjhmkoqkqf0ohbocl...@mail.gmail.com> > Content-Type: text/plain; charset="windows-1252" > > > > 1) In a design with group and gender as discrete factors and > age > >> > as a continuous factor, why is it that QDEC only displays the > >> > contrast "Does the avg thickness, accounting for gender, > differ > >> > between group1 and group2?" and not also "..acounting for > gender > >> > and age,.."? > >> > > >> I thought that it would have. Are you coding age as a nuisance > >> variable? > >> Also, are you coding gender as a continuous variable? That is > >> something > >> you should not do. > >> > >> > >> I was not coding age as a nuisance variable but as a continuous variable > >> (co-variate). Gender was a discrete/fixed factor but I'm not sure > whether > >> this means 'continuous' in the sense discussed in your exchange with > Arman. > >> Anyway, in this configuration, it seems gender and age are not accounted > >> (controlled) for at the same time. > >> > > It should be. Can you send your qdec table? > > See attached > > > > > > > >> > 3) From the group tutorial, I see that mris_preproc has to be > >> > called with flag "--cache-in ess.fwhm10thickn.fsaverage". > >> However, > >> > after running recon-all (including with the ?qcache option) > >> on all > >> > my subjects, none of their folders contains a file named > >> > ?h.thickness.fwhm10.fsaverage.mgh > >> > > >> Where does it say to use ess.fwhm10thickn.fsaverage? > >> > >> Sorry, typo. The flag is actually "--cache-in > >> thickness.fwhm10.fsaverage", I file that I do not have after having run > >> recon-all (including with the --qcache option) > >> > > Try running recon-all again with just the --qcache flag. > > This is what I had done previously; the command was: > recon-all -s C${i} -qcache > where the ${i} was a counter in a script, to run the command on all my > subjects > > > > > > > >> > 5) What is the difference between running > >> make_average_subject and > >> > running mris_preproc with --target fsaverage? > >> > > >> make average subject makes the average subject. mris_preproc > >> samples the > >> data into a common space defined by the registration surface and > >> concatenates the input subjects into a single stack. > >> > >> But should the registration surface used by mris_preproc (i.e. its > >> "--target" flag) come from the 'average' subject or from 'fsaverage'? In > >> other words, which one of these becomes the study-specific template? > >> > > You have to tell mris_preproc both the target and the surface > registration > > to use if you want to use a different average subject. > > The command I used is: > > mris_preproc --fsgd group_gender__age.fsgd --target average --hemi rh > --meas thickness --out rh.thickness.mgh > So if I understand correctly, the fact that I didn't indicate a surface > registration means that the surface from the "average" subject will be > used, rather than the one from "fsaverage"? I still don't understand the > difference between those two, and which, if any, can be referred to as the > study-specific template. > > B) All concatenated volumes from mris_preproc's output files > >> (?h.thickness.mgh) appear blank in freeview, even though the individual > >> structurals all look fine. Also, lh.thickness.mgh and rh.thickness.mgh > >> have, surprisingly, *exactly* the same file size, which is also a bit > small > >> (~25MB) to be able to contain 38 registered structurals, which suggests > >> something went wrong... > >> > > These are surface overlay files, not volumes. You can't load surfaces as > > volumes in freeview. > > > So assuming I don't visually inspect the surface overlays, can I assume > that mris_preproc ran fine if lh.thickness.mgh and rh.thickness.mgh have > exactly the same file size? > > > > > C) When running mri_surf2surf, I get an error saying that file > >> /surf/lh.white cannot be opened. The 'average' folder produced after I > ran > >> make_average_subject does not contain a /surf/lh.white file, only a > >> /surf/lh.white_avg file! I didn?t find a log file from > make_average_subject > >> so i don?t know if it gave any errors.. > >> > > It's extremely helpful to have command lines ... > > > > Sorry, my commands were: > make_average_subject --subjects C01 C02 C03 C04 C05 C06 C07 C08 C09 C10 C11 > C12 C13 C14 C15 C16 C17 C18 C19 M01 M02 M03 M04 M05 M06 M07 M08 M09 M10 M11 > M12 M13 M14 M15 M16 M17 M18 M19 > mri_surf2surf --hemi lh --s average --sval lh.thickness.mgh --fwhm 10 > --tval lh.thickness.10.mgh > _________________________ > > Could someone please explain how the following descriptions of a contrast > are exactly linked: > i) a contrast's namesake folder (including keywords 'Avg'/'Diff'/'X' and > 'Intercept'/'Cor'; e.g. > "lh-Diff-group1-group2-Cor-thickness-behaviouralMeasure"), > ii) its phrasing in QDEC ("Does the thickness-age correlation differ > between group1 and group2?"), > iii) the assignment of values to each column of the design matrix, in the > C.dat contrast vector (e.g. [0, 0, 1, -1]) > > _________________________ > (this is actually a bug report) After setting a different FDR threshold and > pressing the "Set Using FDR" button, more often than not the results image > doesn?t change accordingly. I noticed that the button only has an effect > after moving around the QDEC window and/or waiting a minute or so > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130522/9a57d302/attachment-0001.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: qdec.table.dat > Type: application/octet-stream > Size: 1196 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20130522/9a57d302/attachment-0001.obj > > ------------------------------ > > Message: 3 > Date: Wed, 22 May 2013 14:08:44 -0400 > From: Martin Reuter <mreu...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] ERROR in long_mris_slope > To: Catherine Bois <c.b...@sms.ed.ac.uk> > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: <519d09ac.7050...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Cathy, > > it must be something else (I think). The mris_calc command looks weird > ("--label " looks like the label is not passed, but a space instead, it > then thinks 'mul' is a file). > > qdecfinal is your qdec table? Make sure it contains only spaces to > separate the fields. It should have at least these columns > fsid fsid-base time > > also in your command below, why are there "?" before do-label and time? > > Unless you want to use the stack (within subject stack of thickness > values), I would drop the --do-stack (maybe also drop do-avg or whatever > else you don't need). > > For debugging, I would create a directory, place a single subject there, > create a new qdec table with only that subject and try again there. If > it still happens , let me know. > > Best, Martin > > > On 05/20/2013 10:25 AM, Catherine Bois wrote: > > Dear Freesurfer experts, > > > > I am trying to conduct the long_mris_slopes --qdec qdecfinal --meas > > thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack > > ?do-label ?time time --qcache fsaverage command for my longitudinal > > processing. However I keep getting the error message: > > > > mris_calc -o /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh > > --label /directory/baseX/surf/lh.long.thickness-spc.fwhm0.mgh mul 100 > > > > > > mris_calc: > > Sorry, but I seem to have encountered an error. > > While accessing file 'mul', > > > > I read online that this was due to a bug encountered in version 5.1, > > however I recently upgraded to version 5.3 and the error message > > persists. As my Long and base runs have been done in version 5.1 > > still, I was wondering whether in order to fix this problem the long > > and base runs need to be rerun with version 5.3, or whether the error > > I am encountering has another solution/ is caused by another problem > > entirely? > > > > Thank you for your help, > > > > Best Wishes, > > > > Cathy > > > > -- > Martin Reuter, Ph.D. > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreu...@nmr.mgh.harvard.edu > reu...@mit.edu > Web : http://reuter.mit.edu > > > > ------------------------------ > > Message: 4 > Date: Wed, 22 May 2013 14:33:08 -0400 > From: Martin Reuter <mreu...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] ERROR in long_mris_slope > To: Catherine Bois <c.b...@sms.ed.ac.uk>, > "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <519d0f64.2080...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Cathy, > > I think the problem is when there are tabs AND spaces. Only spaces > should also work. I can write some code (when I have time) that checks > these things, maybe for the next release. > > Best, Martin > > On 05/22/2013 02:21 PM, Catherine Bois wrote: > > Hi, > > > > Thank you for your reply. I finally got it working today.thanks for > > your help=)! You say the qdec table should have only spaces; however > > they only seem to work when they are completely tab separated and not > > a single space? If there is accidently a space it will suddenly not > > work. Is there a way that can solve this problem that you can think > > of? It is very time consuming because suddenly it will jsut stop > > working and I need to start from scratch! > > > > > > Quoting Martin Reuter <mreu...@nmr.mgh.harvard.edu> on Wed, 22 May > > 2013 14:08:44 -0400: > > > >> Hi Cathy, > >> > >> it must be something else (I think). The mris_calc command looks > >> weird ("--label " looks like the label is not passed, but a space
_______________________________________________ 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.
