Re: [Freesurfer] Longitudinal processing with windows subsystem for linux (WSL) using ubuntu 18.04.1 LTS

External Email - Use Caution Dear Falk I have no idea, but recognised that the error refers to --qedc and not to --qdec. maybe there is a spelling error somewhere that is related to your problem. HTH Cheers Jürgen

Re: [Freesurfer] [EXTERNAL] Re: extracting FA from FA_skeletonised with freesurfer parcellation

External Email - Use Caution Dear Stephanie what happens with the FA values when you 1. use all_FA map instead of only the skeletonised map (all_FA_skeletonised) 2. did you check whether mri_segstats computes the average while simultaneously excludes voxels of the mask where no

[Freesurfer] Multivariate analysis of covariate with multiple dependent covariates

External Email - Use Caution Dear Statistics Experts we performed a multivariate analysis of covariance (MANCOVA) between two groups using fractional anisotropy (FA), axial diffusivity (AD), radial diffusivity (RD), and mean diffusivity (MD) of the inferior fronto-occipital fas

[Freesurfer] Arcuate fasciculus seed regions in MNI space

External Email - Use Caution Dear tractography experts does anyone have the arcuate fasciculus seed regions in MNI space and is willing to share these seeds with us? we are also interested in MNI space seed regions of the different parts of the SLF (according work done by Catani

Re: [Freesurfer] tractstats2table error

-- > On 19 Dec 2017, at 09:52, Juergen Haenggi > wrote: > > Dear FS and TRACULA experts > > I use FS6 on a Mac and I am trying to extract path statistics using the > tractstats2table command, but faced the following error always for the last > file in the list:

[Freesurfer] tractstats2table error

Dear FS and TRACULA experts I use FS6 on a Mac and I am trying to extract path statistics using the tractstats2table command, but faced the following error always for the last file in the list: …. /dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt is not found or is too small to be a valid s

[Freesurfer] TRACULA and the IFOF

Dear TRACULA experts I am wondering wheter someone has already implemented the tractography of the inferior fronto-occipital fascicle (IFOF) into TRACULA? if yes, we are interested in this implementation. Regards Jürgen Hänggi

[Freesurfer] mris_register vs surfreg

Dear FS experts we constructed a customized template (using make_average_subject) to register the individual surfaces on that template instead of the fsaverage template. we recognized that there are, at least, two ways to do this either using mris_register or using surfreg. Is there any differe

Re: [Freesurfer] Label numbers aparc.a2009s

this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. - Am 03.06.2017 um 06:24 schrieb Juergen Haenggi: > Dear FS experts >

[Freesurfer] Label numbers aparc.a2009s

Dear FS experts I have a question wrt the label numbers in FreeSurferColorLUT.txt compared with those in aparc.a2009s+aseg.mgz. I noticed that the last ctx (GM) label in FreeSurferColorLUT.txt file is 12175 ctx_rh_S_temporal_transverse whereas in the aparc.a2009s+aseg.mgz file, the highest in

Re: [Freesurfer] Error while attempting Segmentation

Hi IPL Neurosurgery it seems that you have no read or write permission to the freesurfer tools. > /home/iplneurosurgery/Documents/freesurfer/mni/bin/nu_correct: Permission > denied. you can change the permission with sudo chmod -R 777 freesurfer Hope this helps Cheers Jürgen

Re: [Freesurfer] Error mri_surf2surf FS6

n you will have to register each individual subject to the target, eg, > > surfreg --s individualsubject --t average_AN_FS6_long_split > > This will create ?h.average_AN_FS6_long_split.sphere.reg which can then > be used in mris_preproc > > > > On 03/09/2017 07:44 A

[Freesurfer] Error mri_surf2surf FS6

Dear FS experts we are trying to run statistics in FS6 Linux. Everthing worked fine until we applied the command mris_preproc that called mri_surf2surf and produced the following error: # ---

[Freesurfer] TRACULA and priors problem

Dear TRACULA experts I run TRACULA FS 6.0 on a Mac and get the following error: #@# Priors Fri Feb 24 17:11:18 CET 2017 /tmp/subj33.interpreter_control_01/.15208.txt: No such file or directory. In the FS archive I found the following email https://www.mail-archive.com/freesurfer@nmr.mgh.harvar

Re: [Freesurfer] FS 6.0 Freeview

Dear FS users I also work with FS6 and MacOSX 10.7.5 and the left upper panel of Freeview does not appear at all, ie.e is empty compared with former Freeview versions (see screenshot). When I load a volume, it also crashed. Both problem appear also on Mac OSX 10.10.5 Thanks in advance Regards

Re: [Freesurfer] aparcstat2label command result does not include corpuscallosum label

Dear Hao Wen the corpus callosum is a subcortical structure and therefore not included in the parcellations. but there are volumetric segmentations of the corpus callosum that can be obtained by using the asegstats2table command. Hope this helps Regards Jürgen ---

Re: [Freesurfer] Ubuntu 16.04 solution?

Dear Niels the way Burkhard suggested works also on our Ubuntu16.04. the new license file must have four lines two of which consists of numbers. you mentioned that your license is the same as for FS 5.3.0. HTH Cheers Jürgen Am 20.10.2016 um 17:57 schrieb NIELS JANSSEN .: > Hi Burkhard, > > Th

Re: [Freesurfer] GLM in groups with unequal size

Dear Eelco years ago i posed a similar question on the FS email list https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021386.html a part of the response is below >>> The other question is how mri_glmfit estimates the variance. Because I have >>> only one subject in the patie

[Freesurfer] Recon-all -long

Dear FS experts Is there any difference or problem when running tp2 on the "longitudinally adjusted" tp1 instead on the recommended cross-sectionaly processed tp1? Thanks in advance Regards Juergen ------- Juergen Haenggi Ph.D

Re: [Freesurfer] cortical thickness

h the > University of Nottingham may be monitored as permitted by UK legislation. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Juergen Haenggi Ph

[Freesurfer] Topology fixer

) ( f=0.00 , v=0.00 , c=3.29 , q= 6.58 ) --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone

[Freesurfer] Voxel-wise analysis of subcortical strucutures

or WM) in the mri folder of the subject, I guess that it is not possible (yet), right? Any advise is appreciated Regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich

[Freesurfer] Problem tkmedit after recon-all -long

accomplish this? Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone

Re: [Freesurfer] Coordinates in tkmedit

chael Harms" <[EMAIL PROTECTED]> wrote: > > Yes, tkmedit shows the image volume in native space. What you are > seeing regarding the corresponding talairach coordinates is consistent > with that. > > cheers, > Mike H. > > On Tue, 2008-10-07 at 16:54 +0200

[Freesurfer] Coordinates in tkmedit

it mean that the image is oblique oriented in the native space? Thanks Regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich

[Freesurfer] Confusion about coordinates in tkmedit

ds Juergen ------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office r

[Freesurfer] Warning in recon-all -long

--- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44

[Freesurfer] Recon-all -long

sequences? Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone

[Freesurfer] Recon-all-long

--- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number

[Freesurfer] FDR button

? Furthermore, this threshold is different when the sig.mgz will be truncated. What does mean the option Only marked? Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology

[Freesurfer] Statistical question

lh --meas thickness --out GCS_lh_thickness_cov_doss.mgh ERROR: flag doss not recognized [Macintosh-3:average/stats/glm] juergenhaenggi% I used FS 4.0.5 for Mac Intel Thanks for help Regards Juergen --- Juergen Haenggi Ph.D. (Dr. des

[Freesurfer] How to show one-tailed t-contrast?

Dear FS experts We have done some FS analysis and would like to show only only the positive contrast. How to do this? We have already run mri_glmfit. Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of

[Freesurfer] Application error

ng I could switch but when trying to switch back the above application error occurred. Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binz

[Freesurfer] Sulcal CSF in aseg

Dear FS experts In the aseg file there are several CSF labels. Does the term "csf" mean sulcal CSF of both cerebral hemispheres, and does the term "restCSF" mean CSF in cisterns? Thanks in advance Best regards Juergen -------

[Freesurfer] Freesurfer vs. VBM in SPM

use FS thickness maps or FS volume maps when comparing FS with classical VBM (SPM, FSL)? Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich

Re: [Freesurfer] lh.aparc.a2005s: S_subcentral_ant label

a FieldName index (analagous to the >>> aseg.stats file) to facilitate detailed accountings of "empty" >>> variables in the ?h.aparc.a2005s files? >>> >>> Many Thanks for any information you can provide, >>> Jenifer >>> >>> ___

[Freesurfer] Black digits and black background

Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041

[Freesurfer] Cannot download new Leopard release

Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041

[Freesurfer] QDEC

] juergenhaenggi% This library is not there. Where can I find this library? Thanks Regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050

[Freesurfer] Vertex-wise thickness correlations

Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44

[Freesurfer] Make_average_subject problem

--- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) [EMAIL

Re: [Freesurfer] Problem make_average_subject

alling mris_preproc with --srcsurfreg, and you do > not have the version of mris_preproc that accepts this flag. You can edit it > to make it --surfreg. Or, you can get a new copy of make_average_surface from: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_sur &

Re: [Freesurfer] Problem make_average_subject

ww.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06641.html). >>> That also returns the same error. >>> >>> Any suggestions? >>> >>> Many thanks, >>> >>> - >>> Jim Porter >>> Graduate Student >>

[Freesurfer] nu_correct not found

exited with ERRORS at Tue Feb 5 08:00:04 CET 2008 [EMAIL PROTECTED] subjects]$ Any idea what is wrong here? Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology

Re: [Freesurfer] Problem make_average_subject

;> Any suggestions? >> >> Many thanks, >> >> - >> Jim Porter >> Graduate Student >> Clinical Science & Psychopathology Research >> University of Minnesota >> >> >> >> >> >> Nick Schmansky wrote

[Freesurfer] Problem make_average_subject

t the descriptor limit to 4096, but the make_average_subject command will not start anymore. Any idea what is wrong here? Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psych

[Freesurfer] Talairach QA check failed

e have experience with scans acquired at 7T and FS? Another question is whether we can run FS with a resolution smaller that 1x1x1mm (larger matrix that 288x288x288)? Thanks in advance Best regards Juergen Haenggi --- Juergen Haenggi Ph.D. (D

Re: [Freesurfer] recon-all times

Linux-centos4_x86_64-stable-pub-v4.0.1 >> >> >> >> TIME: 20.5 h --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Z

Re: [Freesurfer] Memory problems

compiled version that is already executable? Thanks a lot in advance Best regards Juergen On 4.1.2008 23:06 Uhr, "Doug Greve" <[EMAIL PROTECTED]> wrote: > You may have to make it executable > > Juergen Haenggi wrote: >> >> Hi Doug >> >> Th

[Freesurfer] Memory problems

t? Is there any possibility, beside buying more RAM, to run make_average_subject with the available 5 GB RAM? Thanks in advance and Happy New Year Best regards Juergen - Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institu

[Freesurfer] Error message II

). ==== = Thanks Regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich

[Freesurfer] Error message

tem...Linux 130.60.235.1 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:58:04 EST 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Wed Dec 12 03:34:18 CET 2007 How to fix that problem? Thanks in advance Best regards Juergen --- Juergen Haenggi P

[Freesurfer] Error message

Nov 30 12:41:09 CET 2007 What does it mean? How to solve that problem? Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14

[Freesurfer] DODS or DOSS?

design matrix is more appropriate for our data? Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich

[Freesurfer] How to read out wmparc

Dear Freesurfer users Is there a similar function like asegstats2table or aparcstats2table in order to read out wmparc.stats? Thanks Best regards Juergen Haenggi --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of

FW: [Freesurfer] ?h.volume files

gt; I'm a bit worried that you have a dimension mismatch. That shouldn't > happen. > > Bruce > > > On Tue, 11 Sep 2007, Juergen Haenggi, > Psychological Institute wrote: > >> Dear Freesurfer users >> >> I computed ?.volume files by using several comman

[Freesurfer] ?h.volume files

write ?h.volume files. Where can I get these numbers? Is it the file called f created in the Matlab current directory after running read_curv multiplying area times thickness, and write_curv? Thanks in advance Best regards Juergen Haenggi - Juergen

[Freesurfer] Directed contrast in FS group analysis

the second class in the fsgd file? Do the other betas correspond to the variables listed from left to right in the fsgd file? Thanks for your confirmation. Best regards Juergen Haenggi --- Juergen Haenggi Ph.D. (Dr. des.) Division of

[Freesurfer] ?h.volume vertex-wise

Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44

[Freesurfer] Mean cortical thickness as nuisance variable

--- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04

[Freesurfer] F-Test and directed contrasts

can we look which color corresponds to which contrast? We searched for the answer in the archives, but did not find it! Thanks in advance Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psyc

[Freesurfer] ANCOVA model in Freesurfer

ds Juergen ------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (

[Freesurfer] Topological defects

should I wait? Up to which number of vertices involved in a defect I should accept it or manually edit it? Thanks a lot for help Best regards Juergen --- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of

[Freesurfer] Error

/freesurfer/subjects juergenhaenggi$ I use Freesurfer v3.0.5 on Mac OS X Intel Tiger. Thanks a lot in advance Best regards Juergen PS: there was no solution for that problem in the archives --- Juergen Haenggi, Ph.D. student

[Freesurfer] Correction

Dear Freesurfer users In my former email, I meant that I can not change from bash to tcsh shell on Mac OS X. Sorry! Thanks Regards Juergen --- Juergen Haenggi, Ph.D. student Department of Neuropsychology Institute of

[Freesurfer] Two problems

ent03_2002 unrecognized. -Patient03_2002 -all The other problem concerns the selection of the tcsh shell on Mac OS X. I can change from a bash to a tcsh shell. Thanks for help in advance Best regards Juergen ------- Juergen Hae

[Freesurfer] Topology fixing

Juergen -- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76

[Freesurfer] Label folder

called "label". But this directory was there and I guess that Freesurfer itself has deleted the label directory. Does anyone had a similar problem or any idea where the problem is? Thanks a lot in advance Best regards Juergen ------ Juergen Hae

[Freesurfer] Recon-all -i ... command does not create all 10 folders

pipe or to run a evaluation tool? Thanks a lot in advance Best regards Juergen ------ Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Le

WG: [Freesurfer] MRInormalize: could not find any valid peaks

be that the missing folders caused the problem? Thanks in advance Best regards Juergen > > Hi Juergen, > > yes, this usually means the talairach is bad. Either run > without it or fix it manually I guess. > Bruce > On Tue, 19 Dec 2006, Juergen Haenggi, > Psychia

[Freesurfer] MRInormalize: could not find any valid peaks

the cause of my problem? The transformation matrix seems also not OK. Because I have about 250 brains which is the fastest way to fix that problem? Thanks in advance Best regards Juergen --- Juergen Haenggi, Ph.D. student Psychiatric

[Freesurfer] Run Freesurfer on a supercomputer

modifying it? What are potential problems that could occur? Thanks in advance Best regards Juergen -- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland

[Freesurfer] Morphometric indices of the hippocampus

results for the hippocampus in the file! Thanks in advance Best regards Juergen -- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931

[Freesurfer] Morphological measures

always zero!!! What happens? Thanks in advance for clarification Best regards Juergen -- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box

[Freesurfer] Templates in Freesurfer

Juergen -- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76

[Freesurfer] recon-all with more than one subject

-- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44

[Freesurfer] setenv FREESURFER_HOME /usr/local/freesurfer

FREESURFER_HOME? A directory, a file or something else? Thanks for help in advance Best regards Juergen -- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland

[Freesurfer] Red Hat Linux Enterprise

Linux Enterprise! Right? Thanks in advance for helping Best regards Juergen -- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931

[Freesurfer] Freesurfer and Red Hat Enterprise

; Best regards > Juergen > > ---------- > Juergen Haenggi, Ph.D. student > Neuropsychology and Imaging > Division of Psychiatry Research > Psychiatric University Hospital > University of Zurich, Switzerland > P.O. Box 1931 > Lenggstrasse 31, 8032 Zurich > 0041 44 384 26 10 (office