[Freesurfer] error

Dear experts, when I run the "qdec", and the wrong information appear in following: qdec.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory I hope some experts to help me ,thank you very much! -- Bo Xiang State Key Laboratory

[Freesurfer] Extracting ROI information using created label

Hi, We are having some trouble extracting ROI (thickness) information using a label we created. After conducting a group analysis, we drew an ROI label based on the results. We used tksurfer to draw the label (we couldn't do this in freeview, which would freeze for some reason). However, at this

[Freesurfer] freesurfer install

Hi freesurfer， I ?installed the package of freesurfer according to the intruction of freesurfer website. But when I checked whether it was installed successfully, I inputed?the commands following: 1)?tksurfer bert rh pial? Couldn't create output file .xdebug_tksurfersubject is bert hemi

Re: [Freesurfer] mc-bbr

This is not something that was ever ready for use. doug On 3/27/14 3:22 PM, SHAHIN NASR wrote: Hi, For a project in which subjects have repeated head movements, I want to register every TR to anatomical scans separately to reduce the effect of head movement as much as possible. When I

Re: [Freesurfer] Problem about the fMRI Analysis?

Surface-based analysis is an alternative to talairach-based analysis. It does not make sense to do both. Is the AFNI talairach space affine (ie, 12 dof)? If so, then it is possible to undo the resampling to talairach space. You will need to know which space the afni results are in (ie, MNI152

Re: [Freesurfer] Problem about the fMRI Analysis?

Dear Douglas, I do not understand what's your meaning? Yes I think the afni results has already alined to T1.mgz, so it is already in talairach space. I do not know what to do next? As I have two groups subjects. I do not know what to analysis the correlation different between two groups by using s

Re: [Freesurfer] Problem with license for running mris_make_face_parcellation

The output is: -rw-rw-rw- 1 Mahshid users 36 Mar 27 12:37 license.txt ___ Freesurfer mailing list Freesurfer@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

[Freesurfer] mc-bbr

Hi, For a project in which subjects have repeated head movements, I want to register every TR to anatomical scans separately to reduce the effect of head movement as much as possible. When I checked the old posts, I noticed that there has been a code since 2011 ( https://mail.nmr.mgh.harvard.e

Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline

Hi Pedro Sorry, right now the only multiple comparisons corrections implemented in lme are the original Benjamini and Hochberg (1995) FDR procedure (lme_mass_FDR) and a more recent and powerful two-stage FDR procedure (lme_mass_FDR2): Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive

Re: [Freesurfer] Problem with license for running mris_make_face_parcellation

Please provide the output when you type: "ls -l $FREESURFER_HOME/license.txt" on the command line. Thanks. -Zeke On 03/27/2014 02:20 PM, Mahshid Najafi wrote: > Yes it is, and I run it, but still receive the error. > > > On Thu, Mar 27, 2014 at 12:41 PM, Mahshid Najafi

Re: [Freesurfer] Problem with license for running mris_make_face_parcellation

Yes it is, and I run it, but still receive the error. On Thu, Mar 27, 2014 at 12:41 PM, Mahshid Najafi wrote: > Hi Douglas, > I tried > > copying it to > $FREESURFER_HOME/license.txt > > but did not work.. > > > > On Tue, Mar 25, 2014 at 1:30 PM, Mahshid Najafi wrote: > >> Hi, >> >> I have an

Re: [Freesurfer] space conversion in the mri_surf2vol

The mgh file is a surface overlay, not a 3d volume. The nii will be in MNI305 space On 03/27/2014 08:36 AM, charujing123 wrote: > Hi Bruce > It's mri_surf2vol --surfval ./lh.gender_age.thickness.10.mgh --hemi rh > --fillribbon --subject fsaverage --identity fsaverage --template > $SUBJECTS_DI

[Freesurfer] saving labels from the terminal?

Dear Freesurfer experts, I'm new to freesurfer and I'm now trying to get anatomical labels from the Destrieux Atlas. I know that we can easily extract labels using the tksurfer GUI by a couple of mouse clicks (load atlas -- click on one label -- save selected label), but I'm just wondering if ther

Re: [Freesurfer] Problem with license for running mris_make_face_parcellation

Hi Douglas, I tried copying it to $FREESURFER_HOME/license.txt but did not work.. On Tue, Mar 25, 2014 at 1:30 PM, Mahshid Najafi wrote: > Hi, > > I have an openSUSE 12.2 (x86_64) and my freesurfer version is > freesurfer-x86_64-unknown-linux-gnu-stable5-20130513. > > freesurfer-Linu

Re: [Freesurfer] mris_preproc patch download

Hi Doug, I had to "Save file as"... So, that was the download... Backup made and mris_preproc replaced by the new one. Thank you! Andreia Quoting Douglas N Greve : > download the file and copy it into $FREESURFER_HOME/bin and make it > executable (make a backup first) > > > On 03/27/2014 09

Re: [Freesurfer] MNI CONVERSION PROBLEM

I have tried several thing like opening on MriCroN and tkregister as: tkregister2 --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --targ /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --reg /root/trabajo/freesurfer/subjects/s_001/mri/transforms/reg.mni152.1mm.dat -

[Freesurfer] (no subject)

Dear Freesurfer experts, I'm new to freesurfer and I'm now trying to get anatomical labels from the Destrieux Atlas. I know that we can easily extract labels using the tksurfer GUI by a couple of mouse clicks (load atlas -- click on one label -- save selected label), but I'm just wondering if ther

Re: [Freesurfer] (no subject)

mri_annotation2label should do the trick cheers Bruce On Thu, 27 Mar 2014, Qing Yu wrote: Dear Freesurfer experts, I'm new to freesurfer and I'm now trying to get anatomical labels from the Destrieux Atlas. I know that we can easily extract labels using the tksurfer GUI by a couple of mouse cli

Re: [Freesurfer] MNI CONVERSION PROBLEM

try tkmedit -f MNI152 -aux aseg.mgz On 03/27/2014 01:18 PM, Gabriel Gonzalez Escamilla wrote: > I have tried several thing like opening on MriCroN and tkregister as: > > tkregister2 --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz > --targ /root/trabajo/fsl/data/standard/MNI152_T1_1m

Re: [Freesurfer] Problem with license for running mris_make_face_parcellation

Is it world-readable? Run chmod a+r $FREESURFER_HOME/license.txt On 03/27/2014 12:41 PM, Mahshid Najafi wrote: > Hi Douglas, > I tried > copying it to > $FREESURFER_HOME/license.txt > but did not work.. > > > On Tue, Mar 25, 2014 at 1:30 PM, Mahshid Najafi > wrote: > >

Re: [Freesurfer] Cohen's D & Multiple Comparisons

I don't think it makes sense to correct using cohen's d. I've never heard of it at least doug On 03/27/2014 06:31 AM, L. Schweren wrote: > > Dear FreeSurfer experts, > > For my group-level analyses, I created Cohen’s D effect size maps. Now > I looking the different methods to correct for multi

Re: [Freesurfer] MNI CONVERSION PROBLEM

The first one should be correct. How are you visualizing it? What is the command line? On 03/27/2014 04:26 AM, Gabriel Gonzalez Escamilla wrote: > I have used both for the output of mni152reg: > > mri_vol2vol --mov > /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --targ > /root/tr

Re: [Freesurfer] mris_preproc patch download

download the file and copy it into $FREESURFER_HOME/bin and make it executable (make a backup first) On 03/27/2014 09:37 AM, _andre...@sapo.pt wrote: > Hello list, > > I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit > for whole brain analysis. > > The link > http://surfer.nm

[Freesurfer] Fwd: Problem about the fMRI Analysis?

Dear Sir, I get the correlation result between two condition of the functional data by using AFNI( I do not know how to do correlation by using freesurfer). And then I use the bbregister to aline the correlation result (produce by Afni) to the anatomical result produced by using freesurfer(recon-a

[Freesurfer] mri_glmfit-sim error

Hello list, I'm working with FS 5.0.3. When I used 'mri_glmfit-sim --glmdir /home/a/freesurfer/g2.lh/C1 --sim mc-z 5000 4 mc-z.abs --sim-sign abs --cwpvalthresh 0.05 --overwrite' for multiple comparison correction, i got an error message 'cannot find /.../g2.lh/C1/mri_glmfit.log'. I found a mri_g

Re: [Freesurfer] adding time points to longitudinal base template {Disarmed} {Disarmed} {Disarmed}

Thanks Martin, I tried that on version 5.1 and it worked. Regards Koushik From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter Sent: Tuesday, March 25, 2014 9:55 AM To: Govindarajan, Koushik Athreya; freesurfer@nmr.mgh.harvard.e

[Freesurfer] mris_preproc patch download

Hello list, I'm working with FS 5.0 and I'll be using either qdec or mri_glmfit for whole brain analysis. The link http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi#Installation takes me to ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mris_preproc where a script appears. I th

[Freesurfer] recon error

Hi, I got this error while running recon-all : 'imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254ERROR: mpr2mni305 execution abo

Re: [Freesurfer] space conversion in the mri_surf2vol

Hi Bruce It's mri_surf2vol --surfval ./lh.gender_age.thickness.10.mgh --hemi rh --fillribbon --subject fsaverage --identity fsaverage --template $SUBJECTS_DIR/fsaverage/mri/orig.mgz --o test.nii Thanks All the best. Rujing Zha 2014-03-27 charujing123 发件人：Bruce Fischl 发送时间：2014-03-27 20:32

Re: [Freesurfer] space conversion in the mri_surf2vol

Hi Rujing we need your entire command line to know cheers Bruce On Thu, 27 Mar 2014, charujing123 wrote: Dear FS experts, I completed mri_surf2vol converting lh.gender_age.thickness.10.mgh into test.nii based on the fsaverage template. I want to know what space for the two files(*.mgh and *.n

Re: [Freesurfer] how to capture blurred GM/WM junction?

Hi Markus use mris_expand. cheers Bruce On Thu, 27 Mar 2014, Markus Gschwind wrote: Thank you, Doug! One last question:  - Using which command would one construct the "?h.white -1mm surface" and the "?h.white+30%GM surface" for visualisation purposes as in Salat  Figure 1(http://www.sciencedir

[Freesurfer] space conversion in the mri_surf2vol

Dear FS experts, I completed mri_surf2vol converting lh.gender_age.thickness.10.mgh into test.nii based on the fsaverage template. I want to know what space for the two files(*.mgh and *.nii) respectively? Thanks. All the best. Rujing Zha 2014-03-27 charujing123

Re: [Freesurfer] mris_anatomical_stats aparc pial and aparcstats2table

Hi Louis, It didn't work either. This is what shows up in the terminal after running mris_anatomical_stats: mris_anatomical_stats -mgz -f ../stats/rh.aparcpial -b -a ./rh.aparc.annot -c ./aparc.ctab FERNANDORODRIGUES rh pial INFO: assuming MGZ format for volumes. computing statistics for eac

[Freesurfer] Cohen's D & Multiple Comparisons

Dear FreeSurfer experts, For my group-level analyses, I created Cohen's D effect size maps. Now I looking the different methods to correct for multiple comparisons (FDR and MC-simulations), it seems to me they are based on p-values, not on effect sizes. I tried applying FDR-correction in tksur

Re: [Freesurfer] how to capture blurred GM/WM junction?

Thank you, Doug! One last question: - Using which command would one construct the "?h.white -1mm surface" and the "?h.white+30%GM surface" for visualisation purposes as in Salat Figure 1 ( http://www.sciencedirect.com/science/article/pii/S1053811910013261?via=ihub )? Thank you! Markus 2014-03

Re: [Freesurfer] MNI CONVERSION PROBLEM

I have used both for the output of mni152reg: mri_vol2vol --mov /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --targ /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat --inv --o /r