Re: [Freesurfer] trac-all inquiry
hi , I have run this subject again, checking all the processing stages, and still get the same issues. I have placed the new output from the preprocessing stage (this is only 1.4 megabytes as the previous one had 2 preprocessing jobs appended) you can find it here: https://dl.dropboxusercontent.com/u/8209026/prepro.txt as I reminder, one issue I spotted is that the dlabel/diff output does not contain all the files just these anat_brain_mask.bbr.nii.gz anat_brain_mask-vent.bbr.nii.gz aparc+aseg+2mm.bbr.nii.gz aparc+aseg.bbr.nii.gz aparc+aseg_mask.bbr.nii.gz cortex+2mm.bbr.nii.gz cortex+2mm+bs.bbr.nii.gz cortex.bbr.nii.gz lowb_brain_mask.nii.gz notventricles.bbr.nii.gz White-Matter.bbr.nii.gz White-Matter++.bbr.nii.g WHILE FOR THE TRACT RELATED ONES it contains all the relevant file extensions to lh.cst_AS_avg33 lh.ilf_AS_avg33 rh.cst_AS_avg33 but for this one rh.ilf_AS_avg33 (only does he _mni_bbr_cpts_5.txt but does not generate the .nii) any help much appreciated cheers DS On Sat, Nov 16, 2013 at 3:41 PM, David Soto d.s...@imperial.ac.uk wrote: Thanks! for some weird unknown reason the log for the preprocessing file of this subject is unusually big (2.8 megabytes) please get it from this link https://dl.dropboxusercontent.com/u/8209026/Archive.zip cheers ds On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi David - This log only shows output from the -path step and not from the -prep step. The file that's missing should be created during the -prep step, so there's no way to figure out what went wrong without seeing the output from the pre-processing. Please cc the freesurfer list on your reply. Thank you, a.y On Sat, 16 Nov 2013, David Soto wrote: Thanks, please see attachedI only noticed this ERROR: Could not open/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/ dlabel/diff/rh.ilf_AS_avg33_m ni_bbr_cpts_5_std.txt cheers DS On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi David - Can you please send us the trac-all.log file for this subject? Without seeing where it stopped and what error messages there are it's hard to guess what's going on. Thanks, a.y On Fri, 15 Nov 2013, David Soto wrote: Hi - trac-all completed in all my Ps except one and I noticed that the dlabel/diff output does not contain all the files I assessed whether it could be do to poor registration, by checking the aparc+aseg file and looks allright I also checked the registration of FA maps to standard space by freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz dtifit_FA.bbr.nii.gz and seems fine also freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz which also seems fine any ideas pls? thanks! ds On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: I suspect the current problem is caused by poor registration. Have you checked the aparc+aseg and/or the registration from diffusion to anatomical and from anatomical to MNI? On Fri, 16 Aug 2013, David Soto wrote: -- http://www1.imperial.ac.uk/medicine/people/d.soto/ 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. -- http://www1.imperial.ac.uk/medicine/people/d.soto/ -- http://www1.imperial.ac.uk/medicine/people/d.soto/ http://www1.imperial.ac.uk/medicine/people/d.soto/ http://www1.imperial.ac.uk/medicine/people/d.soto/ -- http://www1.imperial.ac.uk/medicine/people/d.soto/ ___ 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] optseq2 for a (sparse) 1-back task
Hi all, I figured I would have some luck tapping expertise on using optseq2 in this mailing list. There are 8 trials times 8 conditions in an event-related design. We are using a 1-back task just to keep participants paying attention. Thus, we are not attempting to match the number of 1-back-yes and 1-back-no trials. In fact, ideally we would have exactly 1 1-back-yes trial for each of the 8 conditions. The plan would be to arrive at a paradigm schedule where, for each of the 8 conditions, there is at least 1 set of consecutive trials for that condition. In this way, if we use only 7 stimuli, then the consecutive trials can use the same item, and that would constitute the 1-back-yes event for that condition as in: 1a1.bmp 2b1.bmp 0NULL 3c1.bmp 2b2.bmp -- 0NULL 2b2.bmp --first instance of consecutive events from same condition assigned same item to create a 1-back-yes event The problem is that I have not discovered any means within optseq to enforce the criterion that at two consecutive events are from the same condition for all 8 conditions. The best I can do is create a large enough pool of paradigm files, and sort through them in the hopes of finding several that meet this requirement. Can optseq2 be forced to meet this requirement, either as a normal command line switch, or else through some clever condition labeling trickery? Thanks, Chris ___ 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] converting cortical labels into volumetric ROIs
btw, you should not need to run mri_annotation2label twice. On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote: Hi all, I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ except since I'm interested in lobe mapping I've changed the first commands, more specifically these are the different command I've run: 1. mri_annotation2label --subject P2 --hemi lh --outdir freeSurfer_Results/P2/labels/ --lobesStrict freeSurfer_Results/P2/labels/freeSurfer_lobes 2. mri_annotation2label --hemi lh --subject P2 --outdir freeSurfer_Results/P2/labels/ --annotation freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s P2 --regheader --reg freeSurfer_Results/P2/register.dat 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 --fillthresh 1 --reg freeSurfer_Results/P2/register.dat the issue I have now is that the final ROI I get (e.g. lh.parietal.nii.gz) looks like a series of disconnected points! I was wondering how I can get a smooth (i.e. filled) volumetric ROI? Thanks, -Mojdeh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] converting cortical labels into volumetric ROIs
use mri_aparc2aseg instead of label2vol. This is how aparc+aseg.mgz is created. Look in the recon-all.log file for the command line used. doug On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote: Hi all, I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ except since I'm interested in lobe mapping I've changed the first commands, more specifically these are the different command I've run: 1. mri_annotation2label --subject P2 --hemi lh --outdir freeSurfer_Results/P2/labels/ --lobesStrict freeSurfer_Results/P2/labels/freeSurfer_lobes 2. mri_annotation2label --hemi lh --subject P2 --outdir freeSurfer_Results/P2/labels/ --annotation freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s P2 --regheader --reg freeSurfer_Results/P2/register.dat 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 --fillthresh 1 --reg freeSurfer_Results/P2/register.dat the issue I have now is that the final ROI I get (e.g. lh.parietal.nii.gz) looks like a series of disconnected points! I was wondering how I can get a smooth (i.e. filled) volumetric ROI? Thanks, -Mojdeh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Re global lgi values
Which above process do you mean? On 11/17/2013 04:57 AM, Anna Jonsson wrote: Thank you. I have tried to write a script to make this above process automatic but it doesn't work. Any tips on how to make the above process into a script for a number of subjects ? Kind Wishes, Anna On Thu, Nov 14, 2013 at 7:39 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: I think it would be --parc aparc.pial_lgi doug On 11/14/2013 11:27 AM, Anna Jonsson wrote: Thank you. Can I then use aparcstats2table --subjects --hemi lh --meas thickness --parc lh.aparc.pial_lgi.stats --tablefile aparc_lgi_lh.txt to get all the values in 1 tablefile or should I use other command? On Wed, Nov 13, 2013 at 6:59 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: yes and yes On 11/13/2013 12:04 PM, Anna Jonsson wrote: Thank you very much. By second I assume you mean second row? And out of the values on the second row it must be the value 2.9472? Is it headed by Area_mm2 or Mean? And what are the units? Thanks again On Wed, Nov 13, 2013 at 4:56 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: that looks correct. It is the 2nd number you want. The first is for the medial wall (not interesting). You can have it report only for cortex by adding --id 1 doug On 11/13/2013 11:45 AM, Anna Jonsson wrote: Dear list, I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using : mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats (Please let me know if this is not correct) I then get this output ( for each individual) ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg 2.4055 0.4052 tel:2.4055%20%20%200.40521.5796 2.9763 1.3967 2 1156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? Thank you very much Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Re: [Freesurfer] Error when using --mask flag in mri_glmfit
This means that there are not enough voxels in the mask to compute the
intervoxel correlation needed to compute the FWHM from the residuals.
The FWHM is needed for clusterwise correction. What does the mask look
like? Does it have a funny shape? If you just want to run mri_glmfit
without the ability to follow up with cluster correction, then add
--no-est-fwhm
doug
On 11/21/2013 08:44 AM, Suzanne Oosterwijk wrote:
Ha, that was my error! Thanks Doug!
Do you have any thoughts on how I can solve the following error when
running glmfit?
FWHM = -nan
ERROR: input FWHM is NaN (not a number).
Check the mask in the glm directory.
I checked the mask from the glm directory using the 2mm version of
fsaverage, and it seems fine.
This is my code:
set labels = (accumb)
foreach label ($labels)
mri_glmfit --y ces.nii.gz --osgm --glmdir glm.${label} --mask
/home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/${label}_lh.mgz
mri_glmfit-sim --glmdir glm.${label} --sim mc-z 1 2.3
mc-z.pos.23.lh --sim-sign pos
end
Best,
Suzanne
On Tue, Nov 19, 2013 at 5:30 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
The label will be totally off because it was not created in the
conformed anatomical space of fsaverage. Does the mask look ok? If
you want to view the label, use something like
tkmedit -f $SUBJECTS_DIR/fsaverage/mri.2mm/orig.mgz -ov sig.mgh
-seg $SUBJECTS_DIR/fsaverage/mri.2mm/aseg.mgz
doug
On 11/19/2013 08:41 AM, Suzanne Oosterwijk wrote:
Hi Doug,
I use the following command to open tkmedit and then I load
the mask, the ocn.mgh file or the original label (created by
mri_binarize) as a segmentation (through the tkmedit menu). In
this case a label does open, but it is totally off.
tkmedit fsaverage orig.mgz -aux brain.mgz -bc-main-fsavg
-overlay
/home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol/omnibus/glm.amygdala/osgm/sig.mgh
-fthresh 2.3 -fmax 4 -aparc+aseg
Thanks!
Suzanne
On Thu, Nov 14, 2013 at 8:48 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
What is your tkmedit command used to view the segmentation?
doug
On 11/14/2013 07:10 AM, Suzanne Oosterwijk wrote:
Hi Doug,
Thanks for the code, this works. Nevertheless, I am a bit
unsure about whether the masks that are used as input into
this command are correct. I like to check all the
stages of
the process and when I open the mask.mgh file within the
appropriate glm folder, the segmentation is totally
off (the
putamen is somewhere in the OFC). Furthermore, even
though the
file that holds the output cluster from the Monte Carlo
simulation (mc-z.pos.23.lh.sig.cluster.mgh) seems
correct, the
segmentation file that I use as input into the
mri_segstats
command is also totally off
(mc-z.pos.23.lh.sig.ocn.mgh) when
I load it in tkmedit. Am I loading it incorrectly as a
segmentation? Does this have anything to do with the
fact that
you advised me to use the 2mm version
fsaverage/mri.2mm/aseg.mgz? Should I adapt for that in my
tkmedit command?
Finally, I also run into a problem with the nucleus
accumbens
specifically. For some reason I get an error when I
run the
glmfit and mc simulation within this specific mask.
First I
make the mask:
mri_binarize --match 26 --i
/home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri.2mm/aseg.mgz
--o
/home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/accumb_lh.mgz
Then I run glmfit:
set labels = (accumb)
foreach label ($labels)
mri_glmfit --y ces.nii.gz --osgm --glmdir glm.${label}
--mask
/home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/${label}_lh.mgz
mri_glmfit-sim --glmdir glm.${label} --sim mc-z 1 2.3
mc-z.pos.23.lh --sim-sign pos
end
But I get an error saying:
FWHM = -nan
ERROR: input FWHM is NaN (not a
[Freesurfer] converting cortical labels into volumetric ROIs
Hi all, I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ except since I'm interested in lobe mapping I've changed the first commands, more specifically these are the different command I've run: 1. mri_annotation2label --subject P2 --hemi lh --outdir freeSurfer_Results/P2/labels/ --lobesStrict freeSurfer_Results/P2/labels/freeSurfer_lobes 2. mri_annotation2label --hemi lh --subject P2 --outdir freeSurfer_Results/P2/labels/ --annotation freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s P2 --regheader --reg freeSurfer_Results/P2/register.dat 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 --fillthresh 1 --reg freeSurfer_Results/P2/register.dat the issue I have now is that the final ROI I get (e.g. lh.parietal.nii.gz) looks like a series of disconnected points! I was wondering how I can get a smooth (i.e. filled) volumetric ROI? Thanks, -Mojdeh ___ 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] recon -all in FS version 5.3 CentOS 6
Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I am wondering up to how many recon -all for separate subjects I can run in parallel. With the version of Snow Leopard 32b I was running two at a time and it took around 20 hours. Would I be able to run 6 subjects in parallel? If so would this process still efficient or there is an optimum number?Thank you,Pablo Date: Wed, 20 Nov 2013 13:11:15 -0500 From: zkauf...@nmr.mgh.harvard.edu To: gariko...@gmail.com CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 I have to agree with Gari, I see no reason for you to not use the CentOS6 build. -Zeke On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :) On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo From: gariko...@gmail.com mailto:gariko...@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablon...@hotmail.com mailto:pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. /PloS one/, /7/(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo From: pablon...@hotmail.com mailto:pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in
Re: [Freesurfer] recon -all in FS version 5.3 CentOS 6
Hi Pablo it depends on how many cores you have Bruce On Thu, 21 Nov 2013, pablo najt wrote: Dear FS experts,I have one question about FS version 5.3 for CentOS 6. I am wondering up to how many recon -all for separate subjects I can run in parallel. With the version of Snow Leopard 32b I was running two at a time and it took around 20 hours. Would I be able to run 6 subjects in parallel? If so would this process still efficient or there is an optimum number? Thank you, Pablo Date: Wed, 20 Nov 2013 13:11:15 -0500 From: zkauf...@nmr.mgh.harvard.edu To: gariko...@gmail.com CC: pablon...@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 I have to agree with Gari, I see no reason for you to not use the CentOS6 build. -Zeke On 11/20/2013 12:52 PM, Garikoitz Lerma-Usabiaga wrote: I have RedHat 6 with Freesurfer 5.3 for CentOS 6, I can't think in any reason to not use this version in your CentOS 6, if you have some other requirements maybe Nick or Zeke could help you better, I am just an user :) On Wed, Nov 20, 2013 at 6:47 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear Gari, Thank you for the advice. One additional question. Considering that I will start from scratch the processing in the CentOS 6, which would be the recommended FS version for CentOS 6? Thanks, Pablo From: gariko...@gmail.com mailto:gariko...@gmail.com Date: Wed, 20 Nov 2013 18:23:40 +0100 To: pablon...@hotmail.com mailto:pablon...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Hi Pablo, you shouldn't mix different OS-s or software version in the same study (Gronenschild, E. H. B. M., Habets, P., Jacobs, H. I. L., Mengelers, R., Rozendaal, N., van Os, J., Marcelis, M. (2012). The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements. /PloS one/, /7/(6), e38234. doi:10.1371/journal.pone.0038234). for the CentOS 6 you should install CentOS 6 (if you want version 4 it works too). regards! Gari On Wed, Nov 20, 2013 at 5:58 PM, pablo najt pablon...@hotmail.com mailto:pablon...@hotmail.com wrote: Dear FS experts, I am forwarding my question (please see below), in case it got lost among the intense flow of messages. Thank you for your consideration. Pablo From: pablon...@hotmail.com mailto:pablon...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Mon, 18 Nov 2013 16:38:41 + Subject: [Freesurfer] Compatibility between RELEASE_I386 i386 and CentOS 6 Dear FS experts, I have a question about compatibility for running recon-all (longitudinal stream) between CentOS 6 x86_64 (64bit) and Mac SnowLeopard OS X 10.6 (32b Intel). I already run recon all- for several of my subjects with a Mac Book Pro with Snow Leopard (using Release_I386 i386). As I have access to an additional machine (a linux CentOS 6 (64b)) I was wondering if I could process additional subjects in parallel with this other machine that are also intended to be included in the longitudinal stream. Also, I am not sure about whether I should be installing in the CentOS 6 machine the software for CentOS 6, or CentOS 4 (32b) because of compatibility issues. Thank you very much for your attention, Pablo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto: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
Re: [Freesurfer] paired analysis question
If you don't have any covariates, you can use --osgm. If you have covariates, then they need to go into an FSGD file. doug On 11/15/2013 04:12 PM, Govindarajan, Koushik Athreya wrote: Hi all, I am trying to compute differences between 2 runs of my same set of subjects (repeatability) using the steps from the paired analysis wiki page. After I finish the mris_preproc and the mri_surf2surf steps, when I do the glmfit, should I be using the osgm option ? Since it is the same subject, I do not need the age variable as mentioned in the 2^nd fsgd file. If I should still be using the 2^nd fsgd file and not osgm, what would my contrast file look like? Thanks for the help Koushik ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Destrieux atlas in FSL
Hi Freesurfer and FSL communities, Firstly, I apologise for the double posting. I suspect there are experts in both groups that can help me. I'd like to be able to visualise the Destrieux atlas that freesurfer uses at the same time as my MNI standard space results in FSL. Is that possible? I'm afraid I've not been successful in my search of the mailing list archives. Thank you for your help. Kirstie -- Kirstie Whitaker, PhD Research Associate tel: +44 7583 535 307 Department of Psychiatry University of Cambridge Herchel Smith Building Robinson Way Cambridge CB2 0SZ ___ 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] recon-all -s subjects -all unexpected termination
Dear professor Bruce, Thanks for your precious prompt. I will try it. All the best. Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-11-21 21:39 主题：Re: [Freesurfer] recon-all -s subjects -all unexpected termination 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing run: recon-all -s subject -make all that will figure out what needs to be rerun and do so. cheers Bruce On Thu, 21 Nov 2013, Rujing Zha wrote: Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly without deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-all again? All the best. 2013-11-21 Rujing Zha ___ 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.
Re: [Freesurfer] help with save_nifti
No idea why. What is the difference in the headers? Can you post the
terminal output of both your mri_vol2surf commands? Also, you can try
using MRIread.m and MRIwrite.m (these use load_nifti and save_nifti
under the hood but also do some things to the header).
doug
On 11/20/2013 08:46 AM, Leila Reddy wrote:
Hi,
I am trying to save a nifti file using save_nifti. I'm running into a
strange problem that I describe below.
I have a nifti file (subj_mask.nii) created by a colleague using
Nibabel (http://nipy.sourceforge.net/nibabel/). This volume is in the
MNI305 space.
Step1: In a first step I wanted to convert this volume to the
fsaverage surface format. To do that I used :
mri_vol2surf --src subj_mask.nii --hemi rh --out_type mgh --float2int
round --o blah9-rh.mgh --projfrac 0.5 --trgsubject fsaverage
--regheader fsaverage.
I load it in tksurfer and when I do view- configure-overlay, I see a
range of values (as expected) and am able to set the min and max
thresholds as I want.
Step 2: In a second step I loaded this nifti file into matlab using
load_nifti and had to alter the volume a little bit as below:
hdr=load_nifti('subj_mask.nii');
vol=hdr.vol;
vol(find(vol4))=0;
hdr.vol=vol;
save_nifti(hdr,'new_mask.nii').
I convert the volume to fsaverage surface space as before but when I
view it in tksurfer I am not able to set a min and max threshold with
configure-overlay. Instead, there is no distribution of values
plotted in the configure overlay window and I get the following error
message: % ERROR updating histo: impossible limits (min 0.6 = max
0.6) for axis x
I finally managed to solve this problem by loading the header
information from a FS-FAST created nifti:
hdr_fsfast = load_nifti('bold/analysis.mni/mask.nii.gz');
hdr_fsfast.vol=vol;
save_nifti(hdr_fsfast,'new_mask.nii').
Now I am able to see the distribution of values in the configure
overlay window and am able to set the thresholds.
The headers for FS-FAST and Nibabel generated niftis are indeed
slightly different but why do I not have the problem in step 1 when I
use the Nibabel file, but only in step 2 after I use save_nifti with
the Nibabel header ?
I use the load_nifti and save_nifti commands very often (and haven't
had problems before because I was only using FS-FAST generated files)
so I would really appreciate it if someone could point out what is
going on so that I understand what to do in future.
Thanks,
Leila
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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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] Warping to MNI space
Do you mean the aseg.mgz for an individual? If so, you can run mni152reg to register that subject to mni152space. Next you can run mri_label2vol to map the aseg to the 152 space. doug On 11/17/2013 07:26 PM, ebell...@uwm.edu wrote: Hello, I plan on using the aseg.nii to create a grey matter mask. I want to warp these grey matter masks to MNI space. I have been trying to use @auto_tlrc in AFNI to do this warping but am having some trouble. The reason I need this in MNI space is because I plan to make a group grey matter mask that I use to restrict my funtional fmri data analysis, which is in MNI space (MNI_avg_152T1). How might I go about doing the warping and I wanted to double check the order of doing things? Should I create the grey matter masks first then warp to MNI? Or do I warp the aseg files to MNI and then create the grey matter masks? Thanks so much! Emily ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] recon-all Process Flow
Hi Rujing sure, you can run them individually if you want. Just make sure it is in the right order and you don't skip any or they will fail cheers Bruce On Thu, 21 Nov 2013, Rujing Zha wrote: Dear all, As we know, recon-all is a integrated code. I have read this code process flow in the website http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. Can I run the a series of command which are presented in command line step by step to realize all the function of recon-all? All the best. 2013-11-21 Rujing Zha Rujing Zhacharujing...@163.com ?2013-11-21 22:30 ???Re:[Freesurfer] recon-all -s subjects -all unexpected termination freesurferfreesurfer@nmr.mgh.harvard.edu ??? Dear professor Bruce, Thanks for your precious prompt. I will try it. All the best. Rujing Zha Bruce Fischl fis...@nmr.mgh.harvard.edu ?2013-11-21 21:39 ???Re:[Freesurfer] recon-all -s subjects -all unexpected termination Rujing Zhacharujing...@163.com ???freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing run: recon-all -s subject -make all that will figure out what needs to be rerun and do so. cheers Bruce On Thu, 21 Nov 2013, Rujing Zha wrote: Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly with out deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-a ll again? All the best. 2013-11-21 _ ___ Rujing Zha ___ 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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly 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.
Re: [Freesurfer] Destrieux atlas in FSL
I think the best thing to do is to just run recon-all on the FSL standard brain doug On 11/21/2013 04:08 PM, Kirstie Whitaker wrote: Hi Freesurfer and FSL communities, Firstly, I apologise for the double posting. I suspect there are experts in both groups that can help me. I'd like to be able to visualise the Destrieux atlas that freesurfer uses at the same time as my MNI standard space results in FSL. Is that possible? I'm afraid I've not been successful in my search of the mailing list archives. Thank you for your help. Kirstie -- Kirstie Whitaker, PhD Research Associate tel: +44 7583 535 307 Department of Psychiatry University of Cambridge Herchel Smith Building Robinson Way Cambridge CB2 0SZ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Cohen'd effect size map
I don't follow the two examples you have there. Why are you reporting a map of Cohen's d? On 11/21/2013 09:40 AM, cj wrote: Dear doug: Thank you for your reply ,and it looks good now.But I meet a question when I am ready to write in my paper,that is how to decribe the annotation of my effect size maps ,I found two papers that were described as follows: 1、Cohen‘s d for the difference between two means was based on sex and age corrected means from a general linear model fitted at each vertex across the cortical surface. 2、The figures present cortical maps of effect sizes (Cohen’s d) based on age-adjusted means from general linear model analyses. Is this right? and which one is better?and is there any cite for it ?and how to describe the pooled standard deviation in the Cohen'd equation,should I write and the pooled standard deviation was based on the residual error standard deviation from the general linear model analyses follow the above two description? Look forward for your answer and thanks a lot! Ji Chen 在 2013-11-08 02:29:38，Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu 写道： I think the gamma/rstd what you want. doug On 11/07/2013 08:14 AM, 陈骥 wrote: Dear freesurfer experts In qdec I use the DODS degsin to obtain the thickness difference between my two groups with age ,gender as nuisance.Then I want to get the effect size map instead of report the significance level. In freesurfer wiki I found that we can obtain the effect size map via gamma/sqrt(gammavar*Npilot), where Npilot is the number subjects in the pilot study.While I have two groups,one control group with 25 subjects and one patient group with 25 subjects too,I doubt that which number I should use ,the number of patient group subjects 25 or for the whole subjects across groups 50 to repalce the Npilot in the equation? And then I look for previous relevant topic in the freesurfer mail list, found that doug suggested that we can get the effect size just use gamma/rstd, I tried for that but found completely different result between I use the equation of gamma/sqrt(gammavar*Npilot), which equation should I use for I want to get the Cohen'd effect size map? Thank you in advance for your helps! Ji Chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cohen'd effect size map
Dear doug: Thank you for your reply ,and it looks good now.But I meet a question when I am ready to write in my paper,that is how to decribe the annotation of my effect size maps ,I found two papers that were described as follows: 1、Cohen‘s d for the difference between two means was based on sex and age corrected means from a general linear model fitted at each vertex across the cortical surface. 2、The figures present cortical maps of effect sizes (Cohen’s d) based on age-adjusted means from general linear model analyses. Is this right? and which one is better?and is there any cite for it ?and how to describe the pooled standard deviation in the Cohen'd equation,should I write and the pooled standard deviation was based on the residual error standard deviation from the general linear model analyses follow the above two description? Look forward for your answer and thanks a lot! Ji Chen 在 2013-11-08 02:29:38，Douglas N Greve gr...@nmr.mgh.harvard.edu 写道： I think the gamma/rstd what you want. doug On 11/07/2013 08:14 AM, 陈骥 wrote: Dear freesurfer experts In qdec I use the DODS degsin to obtain the thickness difference between my two groups with age ,gender as nuisance.Then I want to get the effect size map instead of report the significance level. In freesurfer wiki I found that we can obtain the effect size map via gamma/sqrt(gammavar*Npilot), where Npilot is the number subjects in the pilot study.While I have two groups,one control group with 25 subjects and one patient group with 25 subjects too,I doubt that which number I should use ,the number of patient group subjects 25 or for the whole subjects across groups 50 to repalce the Npilot in the equation? And then I look for previous relevant topic in the freesurfer mail list, found that doug suggested that we can get the effect size just use gamma/rstd, I tried for that but found completely different result between I use the equation of gamma/sqrt(gammavar*Npilot), which equation should I use for I want to get the Cohen'd effect size map? Thank you in advance for your helps! Ji Chen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
Re: [Freesurfer] RAS, MNI305, Talairach, MNI-Talairach?
The Vertex RAS is a FS internal coordinate system Vertex MNI Talairach is the MNI305 coords Vertex Talairach is an estimate of talairach coords based on a transform from Matthew Brett see http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach On 11/18/2013 08:39 AM, Anita van Loenhoud wrote: Hi all, I find myself getting quite confused about different coordinates systems. Is the following correct (when viewing in TkSurfer): RAS=MNI Talairach=MNI305 (they are all the same?) Talairach= (non linear) conversion from MNI305 Thanks, Anita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] problem feeding design matrix to mri_glmfit
Thank you Doug, that worked a treat! I knew it must have been something simple I was missing. Best. LT On Tue, Nov 19, 2013 at 8:45 AM, Douglas N Greve gr...@nmr.mgh.harvard.eduwrote: The problem is with the mat file, not the input. The matrix should be an ascii text file. doug On 11/18/2013 12:09 PM, Laura M. Tully wrote: Hello freesurfers, I'm trying to run mri_glmfit between groups analysis (patients vs. controls) with gender, age, medication (continuous), and duration of illness as covariates. Because the control group have values of zeros for medication and duration of illness (which results in an illconditioned matrix), I have created my own design matrix so that controls do not have a column for medication or duration of illness and am feeding this matrix into mri_glmfit instead of the fsgd file. However, this seems to cause a problem with the --y input; when I try to run mri_glmfit, i get an error message error in uncompressing - I'm not quite sure what this means, perhaps I did something wrong in creating the design matrix? See the full output below. I've also attached the design matrix, contrast file, and the original fsgd (which results in the ill conditioned matrix). Best, Laura. *Command line: * mri_glmfit --y lh_grpDiffs_thickness10.mgh --X new_mat_files/X_lh_grp_thick_med_dur.mat --C Contrast1B_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex --glmdir lh.grp_diffs_thickness_med_dur_112013.glmdir --illcond *Output:* Reading source surface /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/surf/lh.white Number of vertices 163842 Number of faces327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis cmdline mri_glmfit --y lh_grpDiffs_thickness10.mgh --X new_mat_files/X_lh_grp_thick_med_dur.mat --C Contrast1B_grp_Diffs_HCvsSZ_Med_Dur.mtx --surf fsaverage lh --cortex --glmdir lh.grp_diffs_thickness_med_dur_112013.glmdir --illcond sysname Linux hostname ncfws13.rc.fas.harvard.edu http://ncfws13.rc.fas.harvard.edu machine x86_64 user ltully FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh logyflag 0 Xnew_mat_files/X_lh_grp_thick_med_dur.mat usedti 0 labelmask /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.grp_diffs_thickness_med_dur_112013.glmdir IllCondOK 1 ReScaleX 1 DoFFx 0 Creating output directory lh.grp_diffs_thickness_med_dur_112013.glmdir Loading y from /ncf/snp/04/SCORE/freesurfer_analysis/glm_analysis/lh_grpDiffs_thickness10.mgh MatrixReadTxT: could not scan value [1][1] File exists ERROR: in uncompressing MATFILE5: 0 x 0, type 0, imagf 0, name '' File exists unsupported matlab format 0 (unknown) File exists Saving design matrix to lh.grp_diffs_thickness_med_dur_112013.glmdir/Xg.dat *** glibc detected *** mri_glmfit: double free or corruption (out): 0x3b1279c0 *** === Backtrace: = /lib64/libc.so.6[0x3229470d7f] /lib64/libc.so.6(cfree+0x4b)[0x32294711db] mri_glmfit[0x99fea2] mri_glmfit[0x5bcbe3] mri_glmfit[0x433608] mri_glmfit[0x433802] mri_glmfit[0x40f2f7] /lib64/libc.so.6(__libc_start_main+0xf4)[0x322941d994] mri_glmfit(__gxx_personality_v0+0x172)[0x40b2ba] === Memory map: 0040-00b86000 r-xp 0040 00:00 0 00b86000-00c86000 ---p 00b86000 00:00 0 00c86000-26a08000 rwxp 00c86000 00:00 0 35b4b000-3d4fa000 rwxp 35b4b000 00:00 0 [heap] 322900-322901c000 r-xp fd:00 557272 /lib64/ld-2.5.so http://ld-2.5.so 322901c000-322921c000 ---p 322901c000 00:00 0 322921c000-322921d000 r-xp 0001c000 fd:00 557272 /lib64/ld-2.5.so http://ld-2.5.so 322921d000-322921e000 rwxp 0001d000 fd:00 557272 /lib64/ld-2.5.so http://ld-2.5.so 322940-322954d000 r-xp fd:00 557376 /lib64/libc-2.5.so http://libc-2.5.so 322954d000-322974d000 ---p 0014d000 fd:00 557376 /lib64/libc-2.5.so http://libc-2.5.so 322974d000-3229751000 r-xp 0014d000 fd:00 557376 /lib64/libc-2.5.so http://libc-2.5.so 3229751000-3229752000 rwxp 00151000 fd:00 557376 /lib64/libc-2.5.so http://libc-2.5.so 3229752000-3229757000 rwxp 3229752000 00:00 0 322980-3229882000 r-xp fd:00 557399 /lib64/libm-2.5.so http://libm-2.5.so 3229882000-3229a81000 ---p 00082000 fd:00 557399 /lib64/libm-2.5.so http://libm-2.5.so 3229a81000-3229a82000 r-xp 00081000 fd:00 557399 /lib64/libm-2.5.so http://libm-2.5.so 3229a82000-3229a83000 rwxp 00082000 fd:00 557399 /lib64/libm-2.5.so http://libm-2.5.so 3229c0-3229c02000 r-xp fd:00 557398 /lib64/libdl-2.5.so http://libdl-2.5.so
Re: [Freesurfer] converting cortical labels into volumetric ROIs
Thanks! so this is the command I've used: mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/labels/freeSurfer_lobes.nii.gz a couple of question I have now: 1. what lables (numbers) correspond to the 5 main lobes? looking at the FreeSurferColorLUT.txt, I'm assuming the lables I'm interested in are in the range of 1000-1035 (left) and 2000-2035 (right), is this correct? should I now manually add the relevant sections to get the 5 lobes?! or is there an automated way to do this?! 2. also, with mri_label2vol I was using the registration flags to move the labels into the native subject space, but this way (using mri_aparc2aseg) I get the labels in the freeSurfer space! are there options to move the lables? or should I do it as a separate step? if so, could you please tell me which command I should use? sorry for bugging you with so many questions! -M On 11/21/2013 01:42 PM, Douglas N Greve wrote: use mri_aparc2aseg instead of label2vol. This is how aparc+aseg.mgz is created. Look in the recon-all.log file for the command line used. doug On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote: Hi all, I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ except since I'm interested in lobe mapping I've changed the first commands, more specifically these are the different command I've run: 1. mri_annotation2label --subject P2 --hemi lh --outdir freeSurfer_Results/P2/labels/ --lobesStrict freeSurfer_Results/P2/labels/freeSurfer_lobes 2. mri_annotation2label --hemi lh --subject P2 --outdir freeSurfer_Results/P2/labels/ --annotation freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s P2 --regheader --reg freeSurfer_Results/P2/register.dat 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 --fillthresh 1 --reg freeSurfer_Results/P2/register.dat the issue I have now is that the final ROI I get (e.g. lh.parietal.nii.gz) looks like a series of disconnected points! I was wondering how I can get a smooth (i.e. filled) volumetric ROI? Thanks, -Mojdeh ___ 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] recon-all Process Flow
Dear all, As we know, recon-all is a integrated code. I have read this code process flow in the website http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. Can I run the a series of command which are presented in command line step by step to realize all the function of recon-all? All the best. 2013-11-21 Rujing Zha 发件人：Rujing Zhacharujing...@163.com 发送时间：2013-11-21 22:30 主题：Re: [Freesurfer] recon-all -s subjects -all unexpected termination 收件人：freesurferfreesurfer@nmr.mgh.harvard.edu 抄送： Dear professor Bruce, Thanks for your precious prompt. I will try it. All the best. Rujing Zha 发件人：Bruce Fischl fis...@nmr.mgh.harvard.edu 发送时间：2013-11-21 21:39 主题：Re: [Freesurfer] recon-all -s subjects -all unexpected termination 收件人：Rujing Zhacharujing...@163.com 抄送：freesurferfreesurfer@nmr.mgh.harvard.edu Hi Rujing run: recon-all -s subject -make all that will figure out what needs to be rerun and do so. cheers Bruce On Thu, 21 Nov 2013, Rujing Zha wrote: Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly without deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-all again? All the best. 2013-11-21 Rujing Zha ___ 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.
Re: [Freesurfer] recon-all -s subjects -all unexpected termination
Hi Rujing run: recon-all -s subject -make all that will figure out what needs to be rerun and do so. cheers Bruce On Thu, 21 Nov 2013, Rujing Zha wrote: Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly without deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-all again? All the best. 2013-11-21 Rujing Zha ___ 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.
