Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

FsAverage
by Boadu, Osei B 24 Feb '14

24 Feb '14

Hello, When trying to either create a symbolic link or copy the fsaverage folder, I am told that permission has been denied. E.g.: ln -s $FREESURFER_HOME/subjects/fsaverage fsaverage ln: creating symbolic link `fsaverage/fsaverage': Permission denied I'm not sure what I should do. Thanks, Osei

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Resolution information
by 赵越 24 Feb '14

24 Feb '14

Hi all, I got a few copies of freesurfer data from some data base. Is it possible to know the resolution of the MRI images, for example, the brainmask.mgz file, in freesurfer? Thanks,Yue

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Freesurfer, merci de m'ajouter à votre réseau LinkedIn
by Merhoum nadia via LinkedIn 24 Feb '14

24 Feb '14

LinkedIn ------------ Merhoum nadia souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, J'aimerais vous inviter à rejoindre mon réseau professionnel en ligne, sur le site LinkedIn. Merhoum Accepter l'invitation de Merhoum nadia http://www.linkedin.com/e/-qq80um-hs29xztw-21/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Merhoum nadia http://www.linkedin.com/e/-qq80um-hs29xztw-21/rso/326038371/4xV2/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hs29xztw-21/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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(no subject)
by Joshua Lee 24 Feb '14

24 Feb '14

Hello, I noticed that Freesurfer's latest release offers an expert option "added -first_wm_peak flag to mris_make_surfaces, which may aid accurate more white matter surfaces especially in heavily myelinated areas like visual cortex on data that is higher res than 1mm. enable the flag via an expert.opts file." Are these expert options doing something similar to what was done in Lüsebrink, Wollrab, Speck, 2013 in *NeuroImage*, in which they " conforms the data to the minimum voxel size, which is equal in all directions if data with an isotropic resolution is used" Thanks Joshua - Joshua Lee Doctoral Candidate Department of Psychology & Center for Mind and Brain University of California, Davis 530.747.3805

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Re: [Freesurfer] Tracula: from anatomical to diffusion space and FSL probtracx
by Anastasia Yendiki 24 Feb '14

24 Feb '14

Hi Gari - The authors of probtrackx would be able to give you more information on how to normalize probtrackx outputs, but I'd suggest taking a look at the methods section of this paper as an example: S. B. Eickhoff, S. Jbabdi, S. Caspers, A. R. Laird, P. T. Fox, K. Zilles, and T. E. J. Behrens, “Anatomical and Functional Connectivity of Cytoarchitectonic Areas within the Human Parietal Operculum,” J Neurosci, vol. 30, no. 18, pp. 6409–6421, May 2010. Hope this helps, a.y On Mon, 24 Feb 2014, Garikoitz Lerma-Usabiaga wrote: > Thanks Anastasia! > > > On Thu, Feb 6, 2014 at 1:11 AM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Gari - You're talking about thresholding the probtrackx maps, right? > > > Yes > > If so the 20% at which the tracula maps are thresholded by default is probably too high for > probtrackx, I'd try something like 2%. (Tracula is global and probtrackx is local tractography, so > their outputs are different beasts.) > > > OK, thanks! The problem is that at 2% I think the tracts I obtain are too big. I attached a subject example > (S_02) with thresholds at 2%, 5%, 20% and 30% in order to have an idea of what do you think it would be normal. > The file is called tracts.png. > > > Inline image 2 > > > Are the waytotal values very different among subjects? > > > I think there is quite high variability, but I don't know what's normal. In the next figure, values.png, you can > find the values: > - Waytotal values for the two new tracts > - Max values in the tracts after normalizing > - Seed mask size > > Inline image 1 > > > > Are the anatomical seed mask sizes very different? > > I don't think so. They are in values.png as well if you want to take a look. > > > Did you take that into account? Probtrackx will generate X sample paths for each voxel in the seed > mask. > > I didn't take either the waytotal or seed mask or waypoint mask sizes into account when thresholding. How would > you recommend doing that? > > > > Did you threshold the tracula tracts before using them as waymasks? > > Yes, using fslmath I used -thrp 20 first to threshold them and after that I binarize it to create the waypoint. > > > > Thank you very much for your help again, > Gari > > > > a.y > > On Tue, 14 Jan 2014, Garikoitz Lerma-Usabiaga wrote: > > Hi Anastasia, it worked perfectly and I could run probtrack between my anatomical seed > and using waypoints from Tracula tracts. > > I have another doubt right now. The probabilities in each new tract are very different. > I divided every value with waytotal using fslmaths -div in order to normalize them, and > obtained something like this: > subject: S_20, Max Value after normalizing with waytotal: 0.75533 > subject: S_23, Max Value after normalizing with waytotal: 0.27883 > subject: S_25, Max Value after normalizing with waytotal: 0.60251 > subject: S_27, Max Value after normalizing with waytotal: 0.32355 > > > Should I consider the same absolute value for all tracts in order to threshold them or > should I threshold all tracts independently with the 20%? > > I want to check visually the existence of the tract between the anatomical and the > tract, with the same probability across subjects, and afterwards obtain the FA values > in order to correlate with behavior. > > Thanks again! > Gari > > > > > > > > On Mon, Jan 13, 2014 at 7:55 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > > Hi Gari - Yes, fslmaths should be able to do it, with -thrp 20. > > a.y > > On Mon, 13 Jan 2014, Garikoitz Lerma-Usabiaga wrote: > > Thanks Anastasia, I finally got it, I had to do mri_vol2vol > twice to have it > in the diffusion space. > I have an additional question: > I want to create waypoint masks for probtracx from Tracula > tracts (for > example, uncinate). > > Should I use mri_binarize on path.pd.nii to create the mask? > Should I use 20% of the maximum value as the threshold in order > to do so? (a > little help with the command line will be greatly appreciated) > > thanks again! > Gari > > > On Sun, Jan 12, 2014 at 3:08 AM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Has mri/hippo_subfield_in_diffusion_space.nii been > actually > transformed to diffusion space by applying the > anatorig2diff > transformation? I'm assuming that your diffusion data is > not > 0.5mm resolution? You can search for the name of the > transformation in trac-all.log to see examples of how it > is > applied to volumes. > > On Sat, 11 Jan 2014, Garikoitz Lerma-Usabiaga wrote: > > Hi Anastasia,the problem is > with mri/hippo_subfield_in_diffusion_space.nii, > which originally is mri/hippo_subfield.mgz, the > output of running recon-all > -hippo-subfields. So as far as I understand it is > not in anatomical space, > according to MRI info, it is (one example): > - LIA > - 85x97x141 > - 0.5x0.5x0.5 > > So, how could I convert it to the diffussion space > in FSL format in order to > be able to use it in probtrackx? > Should I do 2 steps or 3 steps? > 1.- mri_convert to anatorig space (brainmask.mgz > space, LIA, 256x256x256) > 2.- anatorig2diff in order to change to FSL format > and to diffusion space? > (3.- would be the previous one in two steps, first > from anatorig to anat and > then from anat to diff) > > Any indication of the best programs to do all the > change will be appreciated > (I've seen in trac-all.log that mostly fsl programs > are being used to do the > flips, and then tkregister2 and bbregister for the > registrations) > > Thanks for the help! > Gari > > > > On Sat, Jan 11, 2014 at 1:31 AM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Gari - So if I understand correctly, your > inputs to > probtrackx are: > > mri/hippo_subfield_in_diffusion_space.nii > dmri.bedpostX/merged > dmri.bedpostX/nodif_brain_mask > > If these all come from the output of tracula, > aren't these all > in LAS orientation? > > a.y > > On Thu, 9 Jan 2014, Garikoitz Lerma-Usabiaga > wrote: > > Hi Anastasia,I want to use a > hippocampal > subfield as > a seed in FSL. I am having problems > understanding > how > to change spaces around... > > 1.- Is this command ok? > mri_vol2vol --mov dmri/dtifit_FA.nii.gz > --targ > > mri/hippo_subfield_in_anatomical_space.mgz --inv > --interp > nearest --o > > mri/hippo_subfield_in_diffusion_space.nii --reg > dmri/xfms/anatorig2diff.bbr.dat > --no-save-reg > > 2.- I would like to visualize it in > freeview in > anatomical space to check if it is ok, > if I load > nu.mgz and > hippo_subfield_in_anatomical_space.mgz > and then load > hippo_subfield_in_diffusion_space.nii > with the > registration file > dmri/xfms/anatorig2diff.bbr.dat, > should I visualize it ok? > If I don't register it, they show to be > displaced > (more than expected). > > > 3.- Afterwards I want to run probtracx > with the > following command (my doubt is mainly > about the > files to > use, since FSL files are RAS, > freesurfer > anatomical > are LIA and freesurfer diffusion are > LIA, are all > the > files in the same format and FSL is ok > with it?): > /usr/local/fsl/bin/probtrackx > --mode=seedmask > > -x mri/hippo_subfield_in_diffusion_space.nii -s > dmri.bedpostX/merged -m > dmri.bedpostX/nodif_brain_mask -o > fdt_paths_hippo_subfields > --dir=FSL_ConnResults_Hipp -c 0.2 -S > 2000 > --steplength=0.5 -P 5000 --opd > > many thanks! > Gari > > > > > 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. > > > > > > > > > _______________________________________________ > 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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recon-all subject folder size
by Durai Arasan 24 Feb '14

24 Feb '14

Hi Freesurfer experts, I am successfully running recon-all on my cluster. However I find that the subject folders have sizes ranging from 300mb to 900mb. I grepped all recon-all.log files for "finished without error" and that seemed fine for all subjects. But I would like to know what is the expected subject folder size when you run recon-all (with -all option) starting from a standard MPRAGE T1 image. This might be useful since I have limited control over the cluster nodes where the processing takes place. Thank you Durai On Mon, Feb 17, 2014 at 2:55 AM, Durai Arasan <durai23(a)gmail.com> wrote: > Hi Freesurfer experts, > > so I got this error when I ran recon-all on my cluster. I am really hoping > this is just a case of missing GCC libraries and nothing is wrong with the > Freesurfer installation on the nodes. Kindly confirm this. > > Thank you > > > ********************************************************************************************************************************** > > Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is /****************** > Actual FREESURFER_HOME /************************************** > Linux ***************************** SMP Fri Mar 22 05:41:51 EDT 2013 > x86_64 x86_64 x86_64 GNU/Linux > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_convert) > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_convert) > mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_convert) > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_convert) > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_convert) > mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_convert) > tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by tkregister2_cmdl) > tkregister2_cmdl: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by tkregister2_cmdl) > tkregister2_cmdl: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by tkregister2_cmdl) > mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_make_uchar) > mri_make_uchar: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_make_uchar) > mri_make_uchar: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_make_uchar) > mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_normalize) > mri_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_normalize) > mri_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_normalize) > mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_watershed) > mri_watershed: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_watershed) > mri_watershed: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_watershed) > mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_gcut) > mri_gcut: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_gcut) > mri_gcut: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_gcut) > mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_segment) > mri_segment: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_segment) > mri_segment: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_segment) > mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_label2label) > mri_label2label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_label2label) > mri_label2label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_label2label) > mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_em_register) > mri_em_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_em_register) > mri_em_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_em_register) > mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_ca_normalize) > mri_ca_normalize: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_ca_normalize) > mri_ca_normalize: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mri_ca_normalize) > mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_ca_register) > mri_ca_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_ca_register) > mri_ca_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_ca_register) > mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_ca_label) > mri_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_ca_label) > mri_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_ca_label) > mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_pretess) > mri_pretess: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_pretess) > mri_pretess: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_pretess) > mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_fill) > mri_fill: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_fill) > mri_fill: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_fill) > mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_tessellate) > mri_tessellate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_tessellate) > mri_tessellate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mri_tessellate) > mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' > not found (required by mri_concatenate_lta) > mri_concatenate_lta: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' > not found (required by mri_concatenate_lta) > mri_concatenate_lta: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mri_concatenate_lta) > mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_normalize_tp2) > mri_normalize_tp2: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mri_normalize_tp2) > mri_normalize_tp2: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mri_normalize_tp2) > mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mris_smooth) > mris_smooth: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mris_smooth) > mris_smooth: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mris_smooth) > mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mris_inflate) > mris_inflate: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mris_inflate) > mris_inflate: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mris_inflate) > mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mris_curvature) > mris_curvature: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mris_curvature) > mris_curvature: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mris_curvature) > mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mris_sphere) > mris_sphere: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mris_sphere) > mris_sphere: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mris_sphere) > mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mris_fix_topology) > mris_fix_topology: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mris_fix_topology) > mris_fix_topology: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mris_fix_topology) > mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mris_topo_fixer) > mris_topo_fixer: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mris_topo_fixer) > mris_topo_fixer: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mris_topo_fixer) > mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mris_ca_label) > mris_ca_label: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mris_ca_label) > mris_ca_label: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mris_ca_label) > mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mris_euler_number) > mris_euler_number: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mris_euler_number) > mris_euler_number: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mris_euler_number) > mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' > not found (required by mris_make_surfaces) > mris_make_surfaces: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mris_make_surfaces) > mris_make_surfaces: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mris_make_surfaces) > mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mris_register) > mris_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not > found (required by mris_register) > mris_register: /lib64/libc.so.6: version `GLIBC_2.7' not found (required > by mris_register) > mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mris_volmask) > mris_volmask: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mris_volmask) > mris_volmask: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mris_volmask) > mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' > not found (required by mris_anatomical_stats) > mris_anatomical_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' > not found (required by mris_anatomical_stats) > mris_anatomical_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mris_anatomical_stats) > mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mrisp_paint) > mrisp_paint: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mrisp_paint) > mrisp_paint: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mrisp_paint) > mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' > not found (required by mris_curvature_stats) > mris_curvature_stats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' > not found (required by mris_curvature_stats) > mris_curvature_stats: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mris_curvature_stats) > mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mris_calc) > mris_calc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mris_calc) > mris_calc: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mris_calc) > mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' > not found (required by mri_robust_register) > mri_robust_register: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' > not found (required by mri_robust_register) > mri_robust_register: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mri_robust_register) > mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' > not found (required by mri_robust_template) > mri_robust_template: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' > not found (required by mri_robust_template) > mri_robust_template: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mri_robust_template) > mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_and) > mri_and: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_and) > mri_and: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_and) > mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_or) > mri_or: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_or) > mri_or: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_or) > mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version > `GLIBCXX_3.4.11' not found (required by mri_fuse_segmentations) > mri_fuse_segmentations: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' > not found (required by mri_fuse_segmentations) > mri_fuse_segmentations: /lib64/libc.so.6: version `GLIBC_2.7' not found > (required by mri_fuse_segmentations) > mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not > found (required by mri_segstats) > mri_segstats: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_segstats) > mri_segstats: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_segstats) > /****************/***444 > > mri_convert /********************/***_mp.nii > /*******************/****444/mri/orig/001.mgz > > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > (required by mri_convert) > mri_convert: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > (required by mri_convert) > mri_convert: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > mri_convert) > Linux ************************************ ************************ SMP > Fri Mar 22 ******** EDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s ***444 exited with ERRORS at Mon Feb 17 02:24:00 EST 2014 > > For more details, see the log file > **********************/***444/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > >

2 1

stats from a volume ROI (in diffusion space)
by Garikoitz Lerma-Usabiaga 24 Feb '14

24 Feb '14

Hi, I have some volume ROIs in diffusion space (1-s and 0-s). I would like to obtain, for example, the average FA values in that ROI. I tried using mri_segstats, but it gives me an error, it needs a segmentation volume. mri_segstats --i dmri/dtifit_FA.nii.gz --mask FSL_waypoint2Hipplh.unc_AS_avg33_mni_bbrlh_headHPC/thres_mask5.nii.gz --sum fa.stats If I substitute --i for --seg I obtain a different error. Which command should I use? I tried dmri_pathstats but it is asking for the file length.samples.txt, which I don't have and don't know how to generate. thanks! Gari

2 2

Contrast Vectors
by Jonathan Holt 24 Feb '14

24 Feb '14

Hi all, I humbly ask for an explanation of contrast vectors, specifically what do 0, 1, -1 indicate, exactly? best, Jon

2 1

Brodmann atlas
by Brahim Belaoucha 24 Feb '14

24 Feb '14

Dear Freesurfer's, I am new in using this software, but from what i know is that the Brodmann cortex segmentation should cover the entire cortex, but I obtained the result attached to this message (26 regions). Knowing that I have used "recon-all" to generate it. Is this a bug? Until I recieve your answer accept all my salutations. -- Sincerely, Brahim. PhD Student at University of Nice Sophia Antipolis. Athena Team-project Phone:(+33) 4-9238-7557

2 1

fwhm31+ ?
by Yang, Daniel 24 Feb '14

24 Feb '14

Dear FreeSurfer Experts, In the folder, $FREESURFER_HOME/average/mult-comp-cor/fsaverage/rh/cortex, there are fwhm01-fwhm30. I am wondering why there is no fwhm31+ and how to generate one if needed? (Sorry for two questions) I used a fwhm=25 in qdec and see the error message when doing cluster analysis: ERROR: cannot find $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm36/... I also don't understand why mri_glmfit-sim looks for fwhm36 when I specify fwhm25? Sorry for the multiple questions! Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.yang(a)yale.edu

2 1

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Freesurfer February 2014