Freesurfer December 2015

freesurfer@nmr.mgh.harvard.edu

115 participants
187 discussions

Meaning of resample type in mri_convert
by Gronenschild Ed (NP) 16 Dec '15

16 Dec '15

Hi FreeSurfer developers, Can you please provide information on the resample types "interpolate" and "weighted" which can be specified with option -rt in mri_convert? Cheers, Ed

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Get summary stats for ROI
by Bronwyn Overs 15 Dec '15

15 Dec '15

Hi Freesurfer Mailing List, I have just completed a GLM analysis with monte carlo correction and now have my "cache.th13.abs.sig.cluster.mgh" files showing the significant clusters for a specific contrast. I would now like to get mean cortical thickness values for these ROIs in another unrelated MRI sample. What is the simplest means of mapping these clusters to my other sample so that I can extract the stats? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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PALS B12
by Woo, Jonghye 15 Dec '15

15 Dec '15

I am trying to a brodmann mask using PALS B12 atlas in fsaverage. I used the following command to create the volume from annotation file. I have two questions associated with it. mri_aparc2aseg --s my_subject --annot PALS_B12_Brodmann --o PALS_B12_Brodmann_Mask.nii --annot-table lh_PALS_B12_table.txt 1. When I visualized the mask, it seems that the labels are not corresponding to the regions (the annot-table is not working). Does anyone know this issue? 2. In this case, I only used lh table. Then do I need to use rh table again? What should I to incorporate both lh and rh? Thank you in advance.

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Problem with mri_surf2surf inside mris_preproc
by Ed Vessel 15 Dec '15

15 Dec '15

Hello - I am having a similar error to this post from 2011: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019290.html ...but as far as I can tell, no answer was given to this post. Perhaps I am just not seeing it? I am taking some contrasts that I computed in volume space for a subject and am converting them to surface space for a group analysis. I am running mris_preproc, using the following command: mris_preproc --target fsaverage --hemi lh --out lh.my_Contr.mgh --iv my_Contr.nii reg/freesurfer/anat2exf.register.dat ..but I get the following error in the call to mri_surf2surf: mri_surf2surf --srcsubject ZM --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgs urfreg sphere.reg --tval ./tmp.mris_preproc.3995/ZM.1.mgh --sval ./tmp.mris_preproc.3995/subjsurfvals.mgh --noreshape --no-cortex ERROR: dimension inconsistency in source data Number of surface vertices = 133192 Number of value vertices = 138083 Any advice on what might be causing this issue? Is it possible that I originally created the subject's segmentation using a slightly older version of freesurfer, or that I did manual edits, and this is leading to this inconsistency? Any suggestions on how to get this working? Thanks for your help, Ed -- Ed Vessel Center for Brain Imaging New York University ed.vessel(a)nyu.edu 4 Washington Place, Rm. 156 New York, NY 10003 http://www.cns.nyu.edu/~vessel (212) 998-8217

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Viewing more than one label at once in Freeview?
by Gold, Andrea (NIH/NIMH) [F] 15 Dec '15

15 Dec '15

Hi, I am trying to show 3 aparc labels on the inflated surface, each in a different color, let’s say lh.inferiortemporal, lh.middletemporal and lh.superiortemporal . I have 2 questions: First I ran mris_annotation2label to extract the individual region aparc labels. I can merge them into a single label with mri_mergelabels, but when I do this both regions are in the same color. I alternatively tried mris_label2annot, as follows: mris_label2annot --s fsaverage --h lh --ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab --a LeftTemporal_test --l labels/lh.middletemporal.label --l labels/lh.inferiortemporal.label --l labels/lh.superiortemporal.label Question 1) Should I be concerned that it says “bankssts, caudalanteriorcingulate, and caudalmiddlefrontla” in the output (copied below) and the freeview windw (see attached) even though I see ITG/MTG/STG on the brain in free view? Question 2) But, when I show the annotation file on the inflated brain in freeview, I can see the three region in 3 different colors, but the rest of the brain is a dark purple and hard to see. See attached image. Is there a way to change this so it looks like the inflated brain typically does? Or, is it possible to view more than one individual label at once? Thanks, Andrea [goldal2@biowulf label]$ mris_label2annot --s fsaverage --h lh --ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab --a LeftTemporal_test --l labels/lh.middletemporal.label --l labels/lh.inferiortemporal.label --l labels/lh.superiortemporal.label Reading ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab Number of ctab entries 36 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /gpfs/gsfs3/users/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label cmdline mris_label2annot --s fsaverage --h lh --ctab /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab --a LeftTemporal_test --l labels/lh.middletemporal.label --l labels/lh.inferiortemporal.label --l labels/lh.superiortemporal.label sysname Linux hostname biowulf.nih.gov machine x86_64 user goldal2 subject fsaverage hemi lh SUBJECTS_DIR /data/EDAN/freesurfer/buckner_data/tutorial_subjs ColorTable /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/aparc.annot.ctab AnnotName LeftTemporal_test nlables 3 LabelThresh 0 0.000000 Loading /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/surf/lh.orig 1 2647065 bankssts 2 10511485 caudalanteriorcingulate 3 6500 caudalmiddlefrontal Mapping unhit to unknown Found 147704 unhit vertices Writing annot to /data/EDAN/freesurfer/buckner_data/tutorial_subjs/fsaverage/label/lh.LeftTemporal_test.annot Andrea Gold, Ph.D. Section on Development and Affective Neuroscience National Institute of Mental Health Room 201, Bldg. 15K, MSC 2670 Bethesda, MD 20892-2670 Phone: 301-827-9804 Fax: 301-402-2010 Email: andrea.gold(a)nih.gov<applewebdata://D38F487B-BA2B-4BF6-A9C4-96248AB2BE51/andrea.gold@nih.gov>

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Segmentation comparison between FS5.3 and FS6beta
by Matthieu Vanhoutte 15 Dec '15

15 Dec '15

Dear FS's experts, I have tried the recon-all process on one subject with both FS v5.3 and v6_beta. Although subcortical structures seems to be better segmented in v6_beta, I find that v6_beta over-segmented some other structures as cerebellum, hippocampus, ... I will attached in the FileDrop my T1.mgz, and aparc.a2009s+aseg.mgz files for both freesurfer versions. Could you please look at it and tell me what do you think about and advise me ? Thank you ! Best regards, Matthieu

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R: Re: recon-all base error
by salvatoreandrea.92＠libero.it 15 Dec '15

15 Dec '15

I have 4 Gb, but I tried with a more poweful machine in the hospital and I got a similar error. I actually think there is a problem of alignment because the 3 T1s are quiet different from each other: they come from a patient affected by MS with a big lesion in the left frontal lobe. This lesion withdraws drastically in the last T1 as you can see from the two attachments. Moreover, I got a problem in the recon-all, given that freesurfer was not able to reconstruct properly the pial and white surfaces (the gray matter is spared in the patient, however it is not included in the lh.pial surf). Do you think there is a way to edit the brainmask for such a big lesion? Would this solve the problems with the recon-all base? Thank you! ----Messaggio originale---- Da: theniels(a)gmail.com Data: 15-dic-2015 9.31 A: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] recon-all base error Hi - how much memory do you have on your machine? On Mon, Dec 14, 2015 at 10:54 AM, salvatoreandrea.92(a)libero.it <salvatoreandrea.92(a)libero.it> wrote: Hi Freesurfer experts! I tried to run recon-all base for a longitudinal analysis on my data. But I get the following error: Excessive topologic defect encountered: could not allocate 221309241 edges for retessellation Cannot allocate memory Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/LinuxI tried with a more powerful pc but I encountered the same problem. Following further information: SUBJECT template_base DATE ven 11 dic 2015, 08.17.47, CET USER salvatore HOST salvatore-HP-630-Notebook-PC PROCESSOR x86_64 OS Linux Linux salvatore-HP-630-Notebook-PC 3.19.0-39-generic #44~14.04.1-Ubuntu SMP Wed Dec 2 10:00:35 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /home/salvatore/freesurfer/bin/recon-all PWD /home/salvatore/freesurfer/subjects/template_base/scripts CMD mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 template_base lh _______________________________________________ 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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dmri_motion tracula timepoint to timepoint motion, or timepoint to reference?
by Ruth Carper 15 Dec '15

15 Dec '15

Hi, I'm hoping to use the dmri_motion tool to quantify motion for some diffusion data that did not use the eddy_correct tool. We have registration matrices that we've successfully reformatted, but I've been scanning the FreeSurfer forum and see some conflicting information about whether the input to dmri_motion should reflect registration of each time point to a single reference orregistration of each time point to the preceding time point. i.e. t0-t1, t0-t2, t0-t3, .... vs. t0-t1, t1-t2, t2-t3, ... What input does dmri_motion expect? I think it's the former but the confusion arises from this post: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41541.html5… ... Of our 4 motion measures, the rotation and translation are computed from the output of the eddy correction (which computes relative displacement from one volume to the next), and the intensity drop-out measures are computed from the raw uncorrected images (because the subsequent corrections will introduce some blurring and might lead to underestimation of the drop-out in each slice). So all measures are computed prior to B0 correction. Hope this helps, a.y But, the contents of the “eddy_correct” command appears to register each time point to a single reference time point. We’re using timepoint 1, i.e. b=0. From the text of Yendiki et al., 2013, I suspect that dmri_motion takes an input that is each timepoint to a single reference timepoint, but outputs a summary that is based on each timepoint to the immediately preceding timepoint? Can you clarify what input does dmri_motion expect? Thanks! Ruth Carper, PhDResearch Assistant Professor, SDSU

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TRACULA NaN values in stats files and empty stats file
by denizzgursel 15 Dec '15

15 Dec '15

Dear Tracula users, I reconstructed uncinate fasciculus using the latest version of Freesurfer and Tracula. However, there seems to be a problem with produced stats files in dpath folder . I have -nan values for the center_avg variables in the file "pathstats.overall.txt" and there is no entry at all for the file "pathstats.byvoxel.txt", it is basically empty. Do you know why this could be happened? Files look like this: pathstats.overall.txt Count 1500 Volume 35 Len_Min 35 Len_Max 35 Len_Avg 35 Len_Center 0 AD_Avg 0.000935047 AD_Avg_Weight 0.000935047 AD_Avg_Center -nan RD_Avg 0.000682719 RD_Avg_Weight 0.000682719 RD_Avg_Center -nan MD_Avg 0.000766828 MD_Avg_Weight 0.000766828 MD_Avg_Center -nan FA_Avg 0.224986 FA_Avg_Weight 0.224986 FA_Avg_Center -nan pathstats.byvoxel.txt # pathway start x y z AD RD MD FA AD_Avg RD_Avg MD_Avg FA_Avg # pathway end Thanks a lot for your help! -- D.

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ERROR: Could not create directory
by jupiter 15 Dec '15

15 Dec '15

Hi, I am running freesurfer 6.0 beta with cuda 6.5 and FSL 5.0.9 on Linux platform, I've got following error: $ trac-all -path -c /scratchTRAC_TEST/dmrirc_first_exp_2.example ......... INFO: Found 8 baseline images (b = 0) out of a total of 136 frames INFO: Found 169534 voxels in brain mask INFO: Resolution of DWI space relative to base space is (1, 1, 1) Loading atlas reference volume from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz Loading affine registration from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dmri/xfms/diff2mni.bbr.mat Loading segmentation map from /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dlabel/mni/aparc+aseg.nii.gz Creating output directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr ERROR: Could not create directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr Linux m2cvlnode17 2.6.32-504.16.2.el6.x86_64 #1 SMP Wed Apr 22 06:48:29 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux The directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath is fully acceptable, I even tried manually create the directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr, then run the command, it deleted /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr, and never created it even the message was "Creating output directory /scratch/TRAC_TEST/First_Exp/First_Exp_Tracula/JA/dpath/lh.cst_AS_avg33_mni_bbr". Could it be a bug or could it be some thing I am missing? Appreciate clues to fix it. Thank you. Kind regards, - ju

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Freesurfer December 2015