Freesurfer

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Re: [Freesurfer] Freesurfer Digest, Vol 141, Issue 48
by Bishesh Khanal 30 Nov '15

30 Nov '15

> Message: 14 > Date: Mon, 30 Nov 2015 09:32:54 -0500 > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] long run fails for new time-point when > removing a tpt that was added with -addtp option > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <565C5E16.3060301(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="windows-1252" > > Hi Bishesh, > > Disclaimer up front: > You probably know that adding time points without re-creating the base > is dangerous (as you bias you analysis, because not all time points are > treated the same). > > Thanks Martin. Yes I understand that but I'm trying to use recon-all in a different setting. For e.g. if I want to compare FreeSurfer results on repeat scans: new1 and new2 both taken on the same day, I understand that ideally one would do two different long runs by including new1 and new2 separately during the creation of base template and then compare the results. However, in my case instead of just new1 and new2, I have several of them that are simulated using different methods and these simulated images will be very close to the images that were already used during the base template creation. So I did not want to recreate the base template for each of these several cases. I want to analyse results on these new1, new2, new3, ..., newN simulated scans of the "same time-point" image but with different methods without recreating the base-template and providing the identical scenario for each of these new1, new2, ..., newN images in long-run. > Now here is why you see the error. > The way a new time points get added to an existing base is this: > 1. register the new time point's norm.mgz to the base norm.mgz (using > mri_robust_register and creates the lta files in mri/transforms) > 2. create a new temporary base norm.mgz from all time points and diff > with existing base norm.mgz > 3. report difference (the idea is to decide if the difference is small > then everything is fine and if it is large, recommend to re-run the base > from scratch, this is not implemented yet and you only see output and it > will always go through) > 4. add the new time point id to the list in base/base-tps > > So for step 3 it needs the norm.mgz from all other time points, to > re-create a temporary norm in the base. > > Now, how can you achieve what you want. I can think of two options: > - edit the base-tps and remove the line with new1 > this should work, the additional transforms to and from new1 (in > base/mri/transforms) can be left behind as they will not be used (you > can also delete those if you like) > - create two copies of the original base (before adding any time > points), then add each time point to each of the two copies. This is > absolutely safe as you make sure that new1 does not affect anything when > adding new2. > Yes if I had only two tpts, copying could be reasonable too, but I have few more, so I'm now considering the first option. Or a quicker way for me could be to temporarily comment out steps 2 and 3 you mentioned above. Could you tell me where in recon-all I could do that ? Thanks, Bishesh > > Anyway, I don't see why anyone would want to do what you are trying to > do, but good luck. > > Best, Martin > > On 11/30/2015 05:53 AM, Bishesh Khanal wrote: > > Hello, > > I had run a longitudinal run by creating a base template with a set of > > time-point scans (tpts). I wanted to add a new tpt (say new1) without > > recreating the base template, hence I used the option -addtp in the > > recon-all -long run. Later on, I no longer needed the results of the > > long run for new1. So I removed the relevant directories for new1 > > (i.e. new1 and new1.long.baseid). > > > > Now I have another tpt (say new2) for which I want a -long run without > > recreating the base template. So I did the same thing as before i.e. > > first a cross run for new2 (which worked fine) and then a long-run > > with -addtp option. However, the long-run for new2 failed with an > > error that it cannot find $SUBJECTS_DIR/new1/mri/norm.mgz > > > > I realize that although I had removed the relevant directories of > > new1, it is still listed in the file $SUBJECTS_DIR/baseid/base-tps. > > However, I do not understand why norm.mgz of new1 is needed by > > recon-all for a long run on new2 when I did not want FreeSurfer to use > > either of new1 or new2 to recreate the base. Ideally, I would want to > > run long run on new1 and new2 under identical conditions. In other > > words, I do not want long-run on new2 tpt to require results from long > > run on new1 tpt. Should it not be the expected behaviour when I am not > > using new1 and/or new2 to create the base template ? > > And, is there a way to do achieve what I want to without manually > > deleting the new1 from the list in the file > > $SUBJECTS_DIR/baseid/base-tps ? > > > > P.S. Initially, the -addtp option had not worked and I had to do the > > following to make it work: > > > > The FreeSurfer version: 5.3.0. Getting around a know bug. in recon-all > > in the following block (around line 6148) > > > > if ( ! $found_tpNid ) then > > echo "ERROR: $tpNid is not in > > ${longbasedir}/${BaseSubjsListFname}" > > echo "" > > exit 1 > > endif > > > > > > replaced the first line (if statement) with: > > > > if ( ! $found_tpNid && ! $DoAddTp ) then > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > >

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R: Re: report a bug
by salvatoreandrea.92＠libero.it 30 Nov '15

30 Nov '15

I have around 2 Gb of total RAM. Isn't that sufficient to run recon-all? If it is not, do you know whether there is a way to split up the process? ----Messaggio originale---- Da: theniels(a)gmail.com Data: 27-nov-2015 17.24 A: "salvatoreandrea.92(a)libero.it"<salvatoreandrea.92(a)libero.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] report a bug Hi - sounds like it's running out of memory and getting killed. How much RAM do you have? On Thu, Nov 26, 2015 at 1:21 PM, salvatoreandrea.92(a)libero.it <salvatoreandrea.92(a)libero.it> wrote: Hi! - I am using Ubuntu 14.4 (trusty). - This is my subject directory: /home/salvatore/freesurfer/subjects - This is the output of which recon-all (that is the tool I am trying to use): /home/salvatore/freesurfer/bin/recon-all - The command line that I run is recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz -all Following the error that I got after 12 hours of processing: sysname Linux hostname salvatore-HP-630-Notebook-PC machine x86_64 setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... Killed Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015, 12.42.40, CET Could you please help me to fix this problem? I tried to ran it again in an other terminal, without succeding...Thank you Best, Salvatore _______________________________________________ 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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error in mri_glmfit-sim using a per-vertex regressor
by Carme Uribe Codesal 30 Nov '15

30 Nov '15

Dear FreeSurfer users, I am trying to add a per-vertex regressor in my general lineal model (a cortical thickness analysis with the white matter-grey matter contrast parameter as regressor). I have no problems with the command line mri_glmfit: mri_glmfit --y rh.cth_corr_MMSE.mgh --fsgd cth_corr_MMSE.fsgd dods --C PDcorr.mtx --pvr rh.wgc_corr_MMSE.mgh --surf fsaverage rh --cortex --glmdir rh.cth_corr_MMSE.glmdir But when I try to run mri_glmfit-sim I think it doesn't consider the regressor (mri_glmfit-sim --glmdir lh.cth_corr_MMSE.glmdir/ --cache 1.3 abs) because I get this warning: *WARNING: unrecognized mri_glmfit cmd option --pvr* *WARNING: unrecognized mri_glmfit cmd option rh.wgc_corr_MMSE.mgh* How can I run the simulation with the regressor? Thank you very much for your help, Carme

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recon-all with more than 10 inputs
by 董昊铭 30 Nov '15

30 Nov '15

Dear freesurfer exports, I am trying to recon more than 10 T1 scans from a single subject, but something went wrong. I have converted all T1 nifti files into mgz format into mri/orig directory with following names: 001.mgz 002.mgz ��. 010.mgz 011.mgz�� But when I run the command: ��recon-all �Cs ${subjec} �Cautorecon1 �Cnotal�Ccheck �Cclean-bm �Cgcut �C no-isrunning -noappend��, it seems that recon-all only recognizes the files with names 01*.mgz(i.e. 0013.mgz), the 00*.mgz(i.e. 001.mgz) files failed to be processed. Once I change the files name to ��001.mgz 002.mgz ��. 0010.mgz 0011.mgz��, the 00*. mgz(i.e. 001.mgz) are able to be recognized, but the 001*.mgz(i.e. 0013.mgz) files failed. How should I deal with this to make all files recognized? Sincerely, Dong Haoming

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long run fails for new time-point when removing a tpt that was added with -addtp option
by Bishesh Khanal 30 Nov '15

30 Nov '15

Hello, I had run a longitudinal run by creating a base template with a set of time-point scans (tpts). I wanted to add a new tpt (say new1) without recreating the base template, hence I used the option -addtp in the recon-all -long run. Later on, I no longer needed the results of the long run for new1. So I removed the relevant directories for new1 (i.e. new1 and new1.long.baseid). Now I have another tpt (say new2) for which I want a -long run without recreating the base template. So I did the same thing as before i.e. first a cross run for new2 (which worked fine) and then a long-run with -addtp option. However, the long-run for new2 failed with an error that it cannot find $SUBJECTS_DIR/new1/mri/norm.mgz I realize that although I had removed the relevant directories of new1, it is still listed in the file $SUBJECTS_DIR/baseid/base-tps. However, I do not understand why norm.mgz of new1 is needed by recon-all for a long run on new2 when I did not want FreeSurfer to use either of new1 or new2 to recreate the base. Ideally, I would want to run long run on new1 and new2 under identical conditions. In other words, I do not want long-run on new2 tpt to require results from long run on new1 tpt. Should it not be the expected behaviour when I am not using new1 and/or new2 to create the base template ? And, is there a way to do achieve what I want to without manually deleting the new1 from the list in the file $SUBJECTS_DIR/baseid/base-tps ? P.S. Initially, the -addtp option had not worked and I had to do the following to make it work: The FreeSurfer version: 5.3.0. Getting around a know bug. in recon-all in the following block (around line 6148) if ( ! $found_tpNid ) then echo "ERROR: $tpNid is not in ${longbasedir}/${BaseSubjsListFname}" echo "" exit 1 endif replaced the first line (if statement) with: if ( ! $found_tpNid && ! $DoAddTp ) then

2 1

Re: [Freesurfer] ERROR: Invalid FreeSurfer license key
by Neda Mohammadi 29 Nov '15

29 Nov '15

Dear Zeke, Hi, My problem was solved, I had 2 .license files that both of them were hidden, it is my fault, sorry. :( *Best Regards,* *Neda*

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FS v.6.0
by Thục Trinh 28 Nov '15

28 Nov '15

Hello Freesurfer experts, I used recon-all command for all my subject by FS v.5.3. But now I decide to upgrade to FS v.6 to eliminate some segmentation errors. The pial errors still appear on the new output of FS v.6 Can I replace the braimask.mgz of FS v.6 by the brainmask.mgz of FS v.5.3 (that been already fixed) to fixed all the pial errors, Have a nice day, Trinh

2 1

problem with cvs_avg35 option in tracula
by Alena Piovar 28 Nov '15

28 Nov '15

Dear Freesurfer experts, I tried to run tracula using cvs registration options (registration to MNI works for me well), but the -prep script crushed, when using cvs_avg35 option. I double checked the configuration file and it seems ok to me. After trying several times, I am still not able to figure out what the problem exactly is. The trac-all.log file is attached. I will be very thankful for any advice or help. Best Alena

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Re: [Freesurfer] ERROR: Invalid FreeSurfer license key
by zkaufman＠nmr.mgh.harvard.edu 28 Nov '15

28 Nov '15

Hello Neda, Hello Neda, Can you please send me an email with a copy of your .license file as an attachment? *Please send it to my direct email address* and not to the Freesurfer support list. I will take a look and send you a valid license file if necessary. -Zeke > Hi Bruce, > > I'm sure about it, but I get the error. > > *Best Regards,* > *Neda* > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] ERROR: Invalid FreeSurfer license key
by Neda Mohammadi 27 Nov '15

27 Nov '15

Hi Bruce, I'm sure about it, but I get the error. *Best Regards,* *Neda*

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