Freesurfer

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30135 discussions

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

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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

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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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report a bug
by salvatoreandrea.92＠libero.it 27 Nov '15

27 Nov '15

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

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Quality Check of Subcortical Segmentation
by Jurij Wiede 27 Nov '15

27 Nov '15

2 1

mris_pmake bilateral
by Silvia Desiree Thielemann 27 Nov '15

27 Nov '15

Dear freesurfer experts, I want to calculate the distance between two vertices which are located on different hemispheres. I was wondering how I could do this with mris_pmake because a hemisphere is required within the analysis. Is there any possibility to obtain the distance between a vertices on the right hemisphere and a vertices on the left hemisphere? I already streamed out the maximum activated voxels which are my start and end vertices. Thanks in advance, Desiree

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Multiple comparisons to confirm atrophy
by Clare Loane 26 Nov '15

26 Nov '15

Dear All, I have completed recon-all on my dataset of controls and patients. My patients have hippocampal/MTL atrophy and I would like to conduct multiple comparisons on the data to ensure that the atrophy is indeed focal in each patient and if not, identify where else atrophy is occurring in these patients. My hypothesis is that I do not expect atrophy elsewhere due to the disease type of these patients, but as this has never been confirmed outside of visual inspection before I wish to check this more robustly. I am not at all familiar with this kind of analysis and would like to ask some advice on how I should approach this? My initial instinct is to go with permutation testing. I would like to consider the whole brain (subcortical and surface). Are there other issues I should be taking into account? Any advice and specific information regarding the subsequent analysis in freesurfer would be greatly appreciated. Many thanks in advance. Clare

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