[Freesurfer] registering functional labels to another anatomical data
Dear experts, I have functional labels registered to Brain A. I also have another anatomical data (Brain B) of the SAME SUBJECT, scanned at a different time. I'd like to calculate cortical thickness of Brain B at those labels, using the functionally defined label that was created with Brain A. Is there a way to convert the functional labels from Brain A to Brain B? Or do I need to re-do the whole functional analysis using the Brain B? Best, Yuko Yotsumoto ___ 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 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] Freesurfer installation problem
Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux. I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the following error message mri_convert /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable. I followed the instruction steps as given in freesurfer wiki. What am I doing wrong here?. Is there a installation wiki page for giving guidelines for ubuntu freesurfer installation. Thanks, any help will be greatly appreciated as I am trying to install freesurfer for the past 3 days without success. Thanks Venkat ___ 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 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.
Re: [Freesurfer] Vol stats of precentral gyrus
Hi everyone, I got in touch last week about asking if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Just wondering if anyone has any thought on this? Many thanks and all the best, Hugh On 6 June 2014 12:00, Hugh Pemberton hughpembert...@gmail.com wrote: Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh On 5 June 2014 12:25, Hugh Pemberton hughpembert...@gmail.com wrote: Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh ___ 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 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] Problem with uploading Cluster Simulation data
Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-4.4.0 and the final analysis with qdec. I have a question concerning the Clusterwise Correction for Multiple Comparison. Is it correct that I have to visualize the results of the Monte Carlo Simulation in freeview? Do I have to upload a special model in freeview before uploading the Cluster Simulation data? Yours sincerely, Carina ___ 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 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.
Re: [Freesurfer] registering functional labels to another anatomical data
Hi Yuko, you can just use mri_label2label to transfer the label from A to B doug On 6/10/14 8:36 AM, Yuko Yotsumoto wrote: Dear experts, I have functional labels registered to Brain A. I also have another anatomical data (Brain B) of the SAME SUBJECT, scanned at a different time. I'd like to calculate cortical thickness of Brain B at those labels, using the functionally defined label that was created with Brain A. Is there a way to convert the functional labels from Brain A to Brain B? Or do I need to re-do the whole functional analysis using the Brain B? Best, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 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] Get thickness of one peak vertex for a group subject
Hi, all. Is there any FS tool for extracting the thickness value of a peak vertex ? From glmfit, I have got the vertex index of the peak. Thanks. Best, Xiang-zhen 【小孔成像】http://www.conxz.net___ 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 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] mri_glmfit for longitudinal 3 group analyses
Hello FS experts, I have 3 groups, e.g : normal, MCI, and AD. Am I correct in my understanding that QDEC would not be applicable here? In my subjectdir, I created a folder for mri_glmfit analyes called FSGD. In that folder, I have the FSDG file and the relevant contrasts. GroupDescriptorFile 1 Class HC Class MCI Class AD input sub1-base MCI input sub2-base AD input sub3-base HC My contrast is a simple [1 0 -1] for HC AD. I called it HC-AD.mtx and saved it in the FSGD folder. Then, in the SUBJECTdir/FSGD folder, I run the mri_glmfit command as follows: mri_glmfit --glmdir fsgd/ --y y.mgh --fsgd g3v0.fsgd --C normal-ad.mtx My question is, what is y.mgh as shown in the examples on the Wiki? It is supposed to be an input file, but what file is this? Thank you very much! Best Regards, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge *| *Department of Psychiatry Trinity College, Cambridge, CB2 1TQ ___ 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 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.
Re: [Freesurfer] registering functional labels to another anatomical data
Hi Yuko sure, you can use mri_robust_register to register them, then give the resulting transform to mri_label2label to map the label from one timepoint to the other. Or you can run them both through the longitudinal stream, in which case the registration etc... will be done for you cheers Bruce On Tue, 10 Jun 2014, Yuko Yotsumoto wrote: Dear experts, I have functional labels registered to Brain A. I also have another anatomical data (Brain B) of the SAME SUBJECT, scanned at a different time. I'd like to calculate cortical thickness of Brain B at those labels, using the functionally defined label that was created with Brain A. Is there a way to convert the functional labels from Brain A to Brain B? Or do I need to re-do the whole functional analysis using the Brain B? Best, Yuko Yotsumoto ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 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.
Re: [Freesurfer] Freesurfer installation problem
Hi Venkat What hardware platform are you running on? And can you run: ls -l /usr/local/freesurfer/bin/mri_convert cheers Bruce On Tue, 10 Jun 2014, Venkateswaran Rajagopalan wrote: Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux. I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the following error message mri_convert /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable. I followed the instruction steps as given in freesurfer wiki. What am I doing wrong here?. Is there a installation wiki page for giving guidelines for ubuntu freesurfer installation. Thanks, any help will be greatly appreciated as I am trying to install freesurfer for the past 3 days without success. Thanks Venkat ___ 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 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.
Re: [Freesurfer] Vol stats of precentral gyrus
Hi Hugh why would any of it be used to produce subcortical volume stats? cheers Bruce On Tue, 10 Jun 2014, Hugh Pemberton wrote: Hi everyone, I got in touch last week about asking if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Just wondering if anyone has any thought on this? Many thanks and all the best, Hugh On 6 June 2014 12:00, Hugh Pemberton hughpembert...@gmail.com wrote: Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh On 5 June 2014 12:25, Hugh Pemberton hughpembert...@gmail.com wrote: Hi everyone, I was wondering if someone could comment on which portion of the precentral gyrus is used to produce subcortical volume stats? Is it just medial or lateral the whole gyrus? Many thanks and all the best, Hugh ___ 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 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] how to extract volumetric measures for dorsal putamen?
Hi Freesurfers, I would like to use in my analysis the volumetric measures for the dorsal putamen. The aseg.stats file generated during recan-all outputs the volume for the whole putamen. I think I will have to manually draw myself a volume of interest including the dorsal putamen. What is the best way to do that? My goal is to get the volumetric measures for the dorsal putamen for each subject so I can include them in my analysis. Thanks! Mihaela ___ 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 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.
Re: [Freesurfer] Freesurfer installation problem
Venkat, Your system appears to be 32bit distribution, as indicated by 'i686' in your output string, but the freesurfer you installed is 64b, indicated by 'x86_64' in our filename. So you will need the 32b dist: freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz Also, v5.0.0 is pretty old, I'd recommend v5.3.0. Nick On Tue, 2014-06-10 at 13:23 +0530, Venkateswaran Rajagopalan wrote: Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux. I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the following error message mri_convert /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable. I followed the instruction steps as given in freesurfer wiki. What am I doing wrong here?. Is there a installation wiki page for giving guidelines for ubuntu freesurfer installation. Thanks, any help will be greatly appreciated as I am trying to install freesurfer for the past 3 days without success. Thanks Venkat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 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.
Re: [Freesurfer] mri_glmfit for longitudinal 3 group analyses
Elijah, Qdec doesnt support three groups, so you'll need to use the commandline. Typing 'mri_glmfit --help' will display some output text. y.mgh is an input file. See also for examples: http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples Nick On Tue, 2014-06-10 at 13:37 +0100, Elijah Mak wrote: Hello FS experts, I have 3 groups, e.g : normal, MCI, and AD. Am I correct in my understanding that QDEC would not be applicable here? In my subjectdir, I created a folder for mri_glmfit analyes called FSGD. In that folder, I have the FSDG file and the relevant contrasts. GroupDescriptorFile 1 Class HC Class MCI Class AD input sub1-base MCI input sub2-base AD input sub3-base HC My contrast is a simple [1 0 -1] for HC AD. I called it HC-AD.mtx and saved it in the FSGD folder. Then, in the SUBJECTdir/FSGD folder, I run the mri_glmfit command as follows: mri_glmfit --glmdir fsgd/ --y y.mgh --fsgd g3v0.fsgd --C normal-ad.mtx My question is, what is y.mgh as shown in the examples on the Wiki? It is supposed to be an input file, but what file is this? Thank you very much! Best Regards, Elijah -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge | Department of Psychiatry Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 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.
Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
Thank you Anthony for the help! I am hoping you don't mind if I ask some more
specific questions for this is pretty new for me.
First off this surface ROI was traced from group results displayed on the
fsaverage. Do I map the label to each individual subject and run the
@SUMA_Make_spec_FS for each subject or should I just run the script on the
label traced off of the fsaverage.
Again thanks for the help this is just all new!
Tara
- Original Message -
From: Anthony Dick ad...@fiu.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Monday, June 9, 2014 10:28:52 AM
Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
Hello all,
I believe Ziad Saad and friends have written AFNI/SUMA to make this
easy. If you run @SUMA_Make_Spec_FS on your freesurfer files, it will
convert all the volume-space segmentation and parcellation files to be
readable in AFNI. Takes only a couple of minutes.
Run @SUMA_Make_Spec_FS -help to see the command line syntax. Look for
the relevant files in the SUMA folder. You can also edit the @SUMA
program to add any file you have newly created that is not a standard
freesurfer file.
Anthony
On 6/9/14, 11:15 AM, Tara Ann Miskovich wrote:
Thank you Paul that is very helpful, but I could use a little more specific
help.
A little more context: I ran a group vertexwise analysis with all my subjects
mapped to the fsaverage and traced my group cluster in QDEC and saved the
label. Now I would like to somehow get it into afni in the same space and use
it for some functional analyses.
I mapped the label to each individual subjects space, but the next step I am
running into issues.
I don't seem to see any medial wall in the aparc annotation. Plus I am not
familiar with the color table, I was just wondering what that would look like.
Any help from anyone would be much appreciated!
Tara
- Original Message -
From: Paul Beach pabea...@gmail.com
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu,
misko...@uwm.edu
Sent: Thursday, June 5, 2014 12:26:00 PM
Subject: Re: [Freesurfer] Freesurfer Surface based ROI to AFNI?
Hi Tara,
I do this regularly, though I don't define my Freesurfer ROIs/labels in QDEC.
The following will do the process into individual subject space
First :
mri_label2label --srclabel path_to_label/label.label --trgsubject {$subj}
--regmethod surface --hemi hemisphere
Do this for as many labels as you have...
Then :
Create a color table file (.ctab file) for each hemisphere that contains your
ROIs. Take a look at the FreesurferColorLUT.txt file for help with that. The
first entry should be the Freesurfer defined medial wall, which you can get
from each subject's aparc.annot via mri_annotation2label.
Then create an annotation file using your .ctab file and your ROIs - one for
each hemisphere
mris_label2annot --s {$subj} --ldir-default --h hemisphere --ctab
hemisphere.ctab_file_name.txt --annot name_for_your_annotation_file \
--l hemi.FS_medial_wall.label \
--l hemi.ROI1.label \
--l hemi.ROI2.label \
--l hemi.ROI3.label \
...
Then create a segmentation file from the annotation file
mri_aparc2aseg --s {$subj} --annot
annotion_you_created_without_hemi_designation --o
segmentation_file_name+aseg.mgz
Then make a gmroi_vol file from which you can extract your ROIs
mri_label2vol --seg segmentation_file_name+aseg.mgz --regheader
segmentation_file_name+aseg.mgz --o you_gmroi_volume.nii.gz --temp
orig/001.mgz
Copy the gmroi_vol to your subject's afni directory
Use 3dcalc to extract individual ROIs from the gmroi_volume. The number you
put in depends on your .ctab file order. The first ROI would be 1001. Like
the ColorLUT, the first digit being '1' is typically for L. hemi, while '2'
would be for the R. hemi.
3dcalc -a your_gmroi_volume.nii.gz -expr 'equals(a,)' -prefix
ROI_name.nii.gz
You can then do your AFNI-based analyses with your ROIs.
Hopefully that's all clear. Let me know if I can help in another way.
Cheers,
Paul
On Thu, Jun 5, 2014 at 12:13 PM, Tara Ann Miskovich misko...@uwm.edu
wrote:
Hi all,
I am wondering if any one has any experience with converting a freesurfer
surface based ROI created in QDEC into a format I could use on functional
data in afni.
Thank you,
Tara
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Anthony Steven
[Freesurfer] Computing LGI values for the longitudinal stream
Dear FS list, I did all 3 steps of the longitudinal stream (cross, base, long), plus the long_mris_slopes for my three-group two-timepoint data set. This gave me files for thickness and area, but I'd also like to do analysis for lGI. To that end, I first did recon-all -s subj -localGI and then recon-all -base subj -tp subj_prescan -tp subj_postscan -localGI These commands ended with the abberantly high lGI value error for 3 subjects out of the total of 72, and for those I then ran what I knew was the standard workaround: recon-all -autorecon2-wm -randomness -autorecon3 -hemi ?h -s subj However received the error It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. I was therefore wondering if it is in fact the case that the longitudinal stream for lGI is done by simply adding -localGI to the normal commands shown in the tutorial http://freesurfer.net/fswiki/FsTutorial/LongitudinalTutorial (i.e. cross, base, long + the long_mris_slopes command)? Also, assuming the lGI values will be eventually be computed as part of the longitudinal stream, are lGI analyses done in the same way as for thickness, i.e. two-stage model and QDEC? Many thanks for any help. Tudor ___ 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 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.
Re: [Freesurfer] Freesurfer installation problem
Hi Bruce, Thanks very much What hardware platform are you running on? Memory: 3.8 GiB Processor Intel core i3-3220 cpu @3.30 GHz*4 Graphics Intel Ivybridge Desktop x86/MMX/SSE2 OS type 32-bit Disk 103.1 GB And can you run: ls -l /usr/local/freesurfer/bin/mri_convert I get the following when the run the above -rwxr-xr-x 1 root root 4015444 May 14 2013 /usr/local/freesurfer/bin/mri_convert Thanks a lot Venkat On Tue, Jun 10, 2014 at 6:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Venkat What hardware platform are you running on? And can you run: ls -l /usr/local/freesurfer/bin/mri_convert cheers Bruce On Tue, 10 Jun 2014, Venkateswaran Rajagopalan wrote: Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux. I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the following error message mri_convert /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable. I followed the instruction steps as given in freesurfer wiki. What am I doing wrong here?. Is there a installation wiki page for giving guidelines for ubuntu freesurfer installation. Thanks, any help will be greatly appreciated as I am trying to install freesurfer for the past 3 days without success. Thanks Venkat ___ 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 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@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.
[Freesurfer] Clusterwise Correction for Multiple Comparisons
Hi, Doug and all, I have two quesiotns about clusterwise correction for multiple comparsion. I run 2 corrections,and commands are as follows: a. mri_glmfit-sim --glmdir g2v0.weight --cache 1.3 abs --cwpvalthresh .05 --2spaces b. mri_glmfit-sim --glmdir g2v0.weight --cache 1.3 pos --cwpvalthresh .05 --2spaces Question 1 : Should the postive clusters from result of command a be same as the result from command b? If yes, why cluster size from reslut of command b is lager than postive cluster from command a in my case?(see results) Resluts form a: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxs Annot 75.208 45661482.74 -6.7 42.3 -22.2 0.01030 0.00900 0.01160 888 medialorbitofrontal 85.103 84832433.13-32.0 30.7 -2.3 0.02270 0.02080 0.02460 1156 lateralorbitofrontal Resluts form b: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWPCWPLow CWPHi NVtxs Annot 16.483 140982864.69-14.8 58.9 -6.1 0.00360 0.00260 0.00479 1416 rostralmiddlefrontal 25.103 84832808.07-32.0 30.7 -2.3 0.00599 0.00459 0.00739 2186 lateralorbitofrontal Question 2 : Is the simulation from pre-cached independent from my results waiting for being corrected? Thanks a lot! Wilder 2014/06/11___ 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 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.
