[Freesurfer] fsaverage_sym in xhemi commands
Dear all, I have a question concerning the xhemi commands as explained here: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi 2. The command surfreg --s $subject --t fsaverage_sym --lh is absolutely searching for fsaverage_sym in the $SUBJECTS_DIR. Do I really have to copy the whole fsaverage_sym folder from $FREESUERFER_HOME/subjects into each subject's directory once again? Thank you very much! Markus ___ 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] Extracting thickness, area and folding values from Qdec
Dear Freesurfer Experts, I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster. I tried to run mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1,3 --sim-sign neg However, I got the ERROR: thresh = 1.3 not completely converted What am I doing wrong? Any other ideas? Is the pdf.dat file the right one to use??? Thanks! DH ___ 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] Longitudinal stream
Dear Freesurfer experts, I would like to perform a longitudinal analysis with freesurfer 5.1 and I have some questions regarding the whole processing stream. I have BL and 1Y follow-up from all patients (110), and moreover I have 2Y follow-up from only some patients (more or less 50). Do you recommend using the 2Y when available in the whole stream? Or, on the other hand, it would be better to perform a BL and 1Y analysis in the whole sample and then, separately, do a second analysis only with those subjects that have 2Y follow-up? My idea is to study rates of change (cortical and ventricles, mainly). I have another more technical question. When running the base (recon-all -base templateid -tp tp1id -tp tp2id ... -all), does the order of the time points matter? In Reuter et al., 2012 says that all scans are treated the same, so I guess it doesn't matter if tp1 is the 1Y and tp2 is the BL. Am I wrong? Finally, to look at ventricle changes, do you also recommend using the longitudinal stream or rather the cross-sectional one? It seems that the longitudinal stream is more cortical specific, but maybe I would be wrong... Thanks Best, Eduard ___ 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] Resting State Networks on Cortical Surface
it is in the 'vol' field
On 03/12/2014 08:54 PM, Xuelong Zhao wrote:
Hmm, it seems I may have misinterpreted the fields in the matlab
structure after using MRIRead
rsn20_surf = MRIread('rsn20_surf.nii')
I thought perhaps the data would be in the 'volsize' field?
rsn20_surf =
srcbext: ''
analyzehdr: []
bhdr: []
vol: [4-D double]
niftihdr: [1x1 struct]
fspec: 'rsn20_surf.nii'
pwd: '~/rsn_smith09'
flip_angle: 0
tr: 1000
te: 0
ti: 0
vox2ras0: [4x4 double]
volsize: [1 139732 1]
height: 1
width: 139732
depth: 1
nframes: 20
vox2ras: [4x4 double]
nvoxels: 139732
xsize: 1
ysize: 1
zsize: 1
x_r: -1
x_a: 0
x_s: 0
y_r: 0
y_a: 1
y_s: 0
z_r: 0
z_a: 0
z_s: 1
c_r: -1
c_a: -17
c_s: 19
vox2ras1: [4x4 double]
Mdc: [3x3 double]
volres: [1 1 1]
tkrvox2ras: [4x4 double]
Date: Wed, 12 Mar 2014 10:55:23 -0400
From: gr...@nmr.mgh.harvard.edu
To: andrewz...@live.com.au
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
You would apply it to the column, row, and slice of a voxel. Note that
the volume structure is volume(row,col,slice). But I'm not sure why
you need to do this. If you read in the ICA maps after running
mri_vol2surf, there will be a value for each vertex, no need to do any
mapping
doug
On 3/11/14 7:00 PM, Xuelong Zhao wrote:
Okay, I think I'm getting close to what I want in the matlab
object. I've successfully imported both the pial surface (using
read_surf.m) and the ICA components on the surface in mgh format
using MRIread.m
I've had a look at the MRIread.m script and it says I can use
vox2ras1 to convert column, row, and slice to XYZ coordinates.
Which field of the matlab structure should I apply this to? Im
guessing its voxels but wanted to make sure, and also I'd have to
do this for each individual frame? Thanks.
Date: Mon, 10 Mar 2014 23:54:18 -0400
From: gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
To: andrewz...@live.com.au mailto:andrewz...@live.com.au
CC: freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
I don't know of anything that will do this (or what a single
object would mean in this case). If you have the overlay in a
volume format (eg, mgz), you can use MRIread.m. This gives you a
value for each vertex, not face, so you'd have to write something
to assign the value to a face.
doug
On 3/10/14 11:27 PM, Xuelong Zhao wrote:
Should also add that I can import the cortical surface into
matlab without any issues using read_surf.m what I would like
to have is the ICA overlay also imported into matlab as
corresponding colors for each face on the cortical mesh. Thanks.
From: andrewz...@live.com.au mailto:andrewz...@live.com.au
To: gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Date: Tue, 11 Mar 2014 11:54:10 +1100
CC: freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical
Surface
Regarding matlab:
Currently, I have in freesurfer the surface extracted via
recon-all. I also have the overlay from running mri_vol2surf
on the ICA components.
I would like to export the pial surface + overlay into matlab
together as a single object. Is there a matlab script for
this, or do I need to do some further processing? Thanks.
Date: Mon, 10 Mar 2014 11:25:23 -0400
From: gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
To: andrewz...@live.com.au mailto:andrewz...@live.com.au
CC: freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Resting State Networks on Cortical
Surface
On 03/09/2014 09:12 AM, Xuelong Zhao wrote:
Hi Doug,
To clarify my previous question:
There is definitely some fuzziness when comparing with the
mov,
whereas the target comparison looks very pristine. I was just
wondering if this is expected. The mov, as
[Freesurfer] 'patching' the base template with additional runs
Dear FS experts, I am trying to add a 6th and 7th timepoint to my longitudinal analysis that already has a base template from 5 timepoints. I saw an earlier response on the mailing list about doing this using a 'patch' script but there was no further information on this. Is this script available in FreeSurfer now ? Thanks Koushik ___ 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] Extracting thickness, area and folding values from Qdec
Use 1.3 not 1,3 doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote: Dear Freesurfer Experts, I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster. I tried to run mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1,3 --sim-sign neg However, I got the ERROR: thresh = 1.3 not completely converted What am I doing wrong? Any other ideas? Is the pdf.dat file the right one to use??? Thanks! DH ___ 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] fsaverage_sym in xhemi commands
Just create a symlink, ie, cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/fsaverage_sym On 03/13/2014 09:57 AM, Markus Gschwind wrote: Dear all, I have a question concerning the xhemi commands as explained here: http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi 2. The command surfreg --s $subject --t fsaverage_sym --lh is absolutely searching for fsaverage_sym in the $SUBJECTS_DIR. Do I really have to copy the whole fsaverage_sym folder from $FREESUERFER_HOME/subjects into each subject's directory once again? Thank you very much! Markus ___ 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] Error mri_label2label
Hi Doug, Thank you very much! It's working! Andreia Quoting Douglas N Greve gr...@nmr.mgh.harvard.edu: Not sure. Try running it with --nohash. It will probably take a lot longer doug On 03/12/2014 02:45 PM, _andre...@sapo.pt wrote: Hello list, When running the following command : mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.thresh.label --trgsubject subjid --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface I get the error INFO: found 1014 nlabel points Performing mapping from target back to the source label *ERROR: srcvtxno = -1 0* trgvtxno = 122050, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table. I have used this command in several subjects and never got this error. What went wrong? As far as I'm aware I did all the processing in the same way for every subject. How can I fix this this? Thank you! Andreia ___ 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
Re: [Freesurfer] Fwd: converting to fsaverage space
Hi -I am trying to extract volumes thickness stats of networks and followed the commands from the post in the subject line to create network .nii files in each subject's space. Based on some other postings, I thought I needed to first move the volumes to surf for each hemisphere, i.e.:mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii --out $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mgh --srcreg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lhBut this does not seem to create the surf correctly - I am unable to load it. I have also tried to use mri_cor2labels to create labels directly front the .nii files but found that the first column in the label files were all -1 (which I found in a previous posting meant the volumes needed to be moved to surface first as I tried above)??I ultimately want to use mris_aatomical_stats with these labels to output stats. Any help would be appreciated,thanks,BarbaraBarbara Weiland, Ph.D.Research Asst. ProfessorCU Change LabDept. of Psychology NeuroscienceUniversity of Colorado Boulderbarbara.weil...@colorado.edu ___ 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] Extracting thickness, area and folding values from Qdec
Dear Doug, I typed 1.3 but it is still not working. Any other ideas??? Thanks for your help. DH Date: Thu, 13 Mar 2014 12:20:57 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec Use 1.3 not 1,3 doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote: Dear Freesurfer Experts, I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster. I tried to run mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1,3 --sim-sign neg However, I got the ERROR: thresh = 1.3 not completely converted What am I doing wrong? Any other ideas? Is the pdf.dat file the right one to use??? Thanks! DH ___ 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] Combining scans with different scanning parameters
Hi Bruce (and others), We can balance the numbers to allow the same number in each configuration. But just to clarify, are you saying we should do, for example, 10 patient scan 1, 10 patient scan 2, 10 patient scan 3, and 10 HC scan 1, 10 HC scan 2, 10 HC scan 3, to perfectly balance everything out? Or do we just need to have X patient and X HC in scan 1, Y patient and Y HC with scan 2, and Z patient and Z HC with scanning parameter 3? Thank you for your assistance. Ashley On Tue, Mar 11, 2014 at 5:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Ashley that is probably trouble unless your groups are perfectly balanced across the datasets (that is, the same # in each group were scanned on each configuration). cheers Bruce On Tue, 11 Mar 2014, Ashley Shurick wrote: Hi, I'm interested in comparing CT differences between 2 different groups, and in order to increase my sample size I'm contemplating combining 3 datasets with different scanning parameters. Some scans were collected with a 3T1 with fmri head coil, while others were collected with a 3T2 magnet with 8 channel head coil. The scans also differ in FOV (25.6 vs 22cm) and resolution. Thank you in advance for your support. Ashley -- Ashley A. ShurickPh.D. Candidate Department of Psychology Stanford University 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. -- Ashley A. Shurick Ph.D. Candidate Department of Psychology Stanford University ___ 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] Combining scans with different scanning parameters
1 would be better but 2 would be sufficient as long as X, Y and Z don't vary too much On Thu, 13 Mar 2014, Ashley Shurick wrote: Hi Bruce (and others), We can balance the numbers to allow the same number in each configuration. But just to clarify, are you saying we should do, for example, 10 patient scan 1, 10 patient scan 2, 10 patient scan 3, and 10 HC scan 1, 10 HC scan 2, 10 HC scan 3, to perfectly balance everything out? Or do we just need to have X patient and X HC in scan 1, Y patient and Y HC with scan 2, and Z patient and Z HC with scanning parameter 3? Thank you for your assistance. Ashley On Tue, Mar 11, 2014 at 5:22 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ashley that is probably trouble unless your groups are perfectly balanced across the datasets (that is, the same # in each group were scanned on each configuration). cheers Bruce On Tue, 11 Mar 2014, Ashley Shurick wrote: Hi, I'm interested in comparing CT differences between 2 different groups, and in order to increase my sample size I'm contemplating combining 3 datasets with different scanning parameters. Some scans were collected with a 3T1 with fmri head coil, while others were collected with a 3T2 magnet with 8 channel head coil. The scans also differ in FOV (25.6 vs 22cm) and resolution. Thank you in advance for your support. Ashley -- Ashley A. ShurickPh.D. Candidate Department of Psychology Stanford University 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. -- Ashley A. ShurickPh.D. Candidate Department of Psychology Stanford University ___ 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] Fwd: converting to fsaverage space
Can you give more details? What is LECN_...nii? Where did it come from? What space is it in? MNI152 I assume? What does it mean you can't load it? Load it with what? What is your command line? doug On 03/13/2014 01:36 PM, Barbara Weiland wrote: Hi - I am trying to extract volumes thickness stats of networks and followed the commands from the post in the subject line to create network .nii files in each subject's space. Based on some other postings, I thought I needed to first move the volumes to surf for each hemisphere, i.e.: mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii --out $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mgh --srcreg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lh But this does not seem to create the surf correctly - I am unable to load it. I have also tried to use mri_cor2labels to create labels directly front the .nii files but found that the first column in the label files were all -1 (which I found in a previous posting meant the volumes needed to be moved to surface first as I tried above)?? I ultimately want to use mris_aatomical_stats with these labels to output stats. Any help would be appreciated, thanks, Barbara Barbara Weiland, Ph.D. Research Asst. Professor CU Change Lab Dept. of Psychology Neuroscience University of Colorado Boulder barbara.weil...@colorado.edu mailto:barbara.weil...@colorado.edu ___ 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] Extracting thickness, area and folding values from Qdec
are you puttting it in quotes? If so, don't doug On 03/13/2014 01:46 PM, Dusan Hirjak wrote: Dear Doug, I typed 1.3 but it is still not working. Any other ideas??? Thanks for your help. DH Date: Thu, 13 Mar 2014 12:20:57 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec Use 1.3 not 1,3 doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote: Dear Freesurfer Experts, I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster. I tried to run mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1,3 --sim-sign neg However, I got the ERROR: thresh = 1.3 not completely converted What am I doing wrong? Any other ideas? Is the pdf.dat file the right one to use??? Thanks! DH ___ 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. -- 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] bvals and bvecs for dt_recon
How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightforward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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] bvals and bvecs for dt_recon
Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in the wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do you have an example? I know how to get those from private dicom tags. Gen -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightforward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen __ __ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] bvals and bvecs for dt_recon
dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (attached). On 03/13/2014 04:50 PM, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in the wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do you have an example? I know how to get those from private dicom tags. Gen -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightforward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen __ __ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer transpose.sh Description: application/shellscript ___ 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] bvals and bvecs for dt_recon
Attached are examples of the bvals.dat and bvecs.dat files extracted from siemens dicoms by dt_recon. This was for a 60 dir DTI scan w/ 10 b0s. On Thu, 13 Mar 2014, Chris Watson wrote: dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (attached). On 03/13/2014 04:50 PM, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in t he wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do yo u have an example? I know how to get those from private dicom tags. Gen -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightfo rward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen __ __ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator The information in this e-mail is intended only for the person to whom it is addressed. If you be lieve this e-mail was sent to you in error and the e-mail contains patient information, please co ntact 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibite d. If you are not the intended recipient, please contact the sender by reply email and destroy al l copies of the original message. If you are the intended recipient, please be advised that the c ontent of this message is subject to access, review and disclosure by the sender's Email System A dministrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.586792 -0.376583 -0.716841 0.894195 0.022917 0.447091 0.729281 -0.410970 0.547041 -0.154251 0.964369 -0.214941 0.117136 0.773539 -0.622830 -0.407575 -0.414994 -0.813427 0.211330 0.753738 0.622269 0.095375 -0.969517 0.225700 -0.135450 -0.033490 -0.990218 -0.142125 -0.750521 -0.645383 -0.637009 0.746109 -0.193757 0.080563 0.971669 0.222192 0.106871 -0.021213 0.994047 0.298747 0.387214 0.872247 -0.207492 -0.803432 0.558072 0.331125 -0.040337 -0.942724 -0.805294 -0.589494 -0.063231 0.337278 -0.749774 -0.569282 0.592396 -0.761390 0.263348 -0.088979 -0.465650 0.880485 -0.527982 -0.430927 0.731803 -0.369111 -0.927082 0.065397 0.311914 0.926381 -0.211018 -0.684511 0.439336 -0.581746 -0.030114 -0.966623 -0.254425 -0.337568 0.744654 -0.575794 -0.574804 0.024806 -0.817915 0.271135 -0.747834 0.605996 -0.935185 0.185421 0.301743 0.889083 0.309665 -0.337104 -0.884343 0.033574 -0.465629 0.545045 0.586317 -0.599298 -0.350774 -0.016274 0.936319 0.416158 -0.900528 -0.125943
Re: [Freesurfer] Fwd: converting to fsaverage space
Hi Barbara, please post to the list. Thanks! the vol2surf command output should be .mgh or .mgz, not .mg (or maybe that is just a typo in the email). If it is, then you should load the mgh file as an overlay, not as a surface, eg tksurfer [subj] lh inflated -overlay file.mgh -fminmax .5 1000 setting the min threshold to .5 assures that you can see the ROI doug On 03/13/2014 05:10 PM, Barbara Weiland wrote: Hi - Sorry to not have been clearer. I have /functional ROIs defined by the Greicius lab// (http://findlab.stanford.edu/functional_ROIs.html) just as in this post to the Freesurfer list from //Mon Dec 2 15:22:08 EST 2013:/ / / Doug, Thank you for your very helpful suggestion. Indeed, doing so made it so I could quickly take any parts (or all) of each Greicius network and put them in individual subject space. In case this may help anyone else, the final series of commands were (in this case, for the whole anterior salience network): *mni152reg --s [subj]* mri_label2vol *--seg anterior_Salience.nii.gz \* --reg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2mm.dat \ --invertmtx --o anterior_Salience_[subj].nii.gz \ --temp $SUBJECTS_DIR/[subj]/mri/orig.mgz Cheers, Paul These ROIs were originally in MNI space and I used the commands listed above from Paul to move them to subject space first creating the reg.mni152.2mm.dat for each subject. LECN….nii is one of these network ROIs. I can see this ROI using free view and it looks correct. What I want is to extract volume and thickness for this ROI. As outlined below,I thought I needed to first convert this to a surface and tried: mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii --out $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mg --srcreg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lh I tried to look at the output (LECN_subjXXX_lh_surf.mg) by using tksurfer [subj] lh inflated and then load the it from the GUI onto the inflated surface -- this says that the file (LECN_subjXXX_lh_surf.mg) has 0 vertices! Probably trying to use a scalar data file as a surface! Do I need to move the LECN….nii to be a surface or should I just be able to make a label from it? I assumed I need the ROI information to be a label to use mris_anatomical_stats? Thank you, Barbara Barbara Weiland, Ph.D. Research Asst. Professor CU Change Lab Dept. of Psychology Neuroscience University of Colorado Boulder barbara.weil...@colorado.edu mailto:barbara.weil...@colorado.edu On Mar 13, 2014, at 1:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you give more details? What is LECN_...nii? Where did it come from? What space is it in? MNI152 I assume? What does it mean you can't load it? Load it with what? What is your command line? doug On 03/13/2014 01:36 PM, Barbara Weiland wrote: Hi - I am trying to extract volumes thickness stats of networks and followed the commands from the post in the subject line to create network .nii files in each subject's space. Based on some other postings, I thought I needed to first move the volumes to surf for each hemisphere, i.e.: mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii --out $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mgh --srcreg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lh But this does not seem to create the surf correctly - I am unable to load it. I have also tried to use mri_cor2labels to create labels directly front the .nii files but found that the first column in the label files were all -1 (which I found in a previous posting meant the volumes needed to be moved to surface first as I tried above)?? I ultimately want to use mris_aatomical_stats with these labels to output stats. Any help would be appreciated, thanks, Barbara Barbara Weiland, Ph.D. Research Asst. Professor CU Change Lab Dept. of Psychology Neuroscience University of Colorado Boulder barbara.weil...@colorado.edu mailto:barbara.weil...@colorado.edu mailto:barbara.weil...@colorado.edu ___ 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 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
Re: [Freesurfer] bvals and bvecs for dt_recon
Thxs for all the help. On March 13, 2014 at 2:19:16 PM, Louis Nicholas Vinke (vi...@nmr.mgh.harvard.edumailto:vi...@nmr.mgh.harvard.edu) wrote: Attached are examples of the bvals.dat and bvecs.dat files extracted from siemens dicoms by dt_recon. This was for a 60 dir DTI scan w/ 10 b0s. On Thu, 13 Mar 2014, Chris Watson wrote: dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (attached). On 03/13/2014 04:50 PM, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in t he wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do yo u have an example? I know how to get those from private dicom tags. Gen -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightfo rward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen __ __ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator The information in this e-mail is intended only for the person to whom it is addressed. If you be lieve this e-mail was sent to you in error and the e-mail contains patient information, please co ntact 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibite d. If you are not the intended recipient, please contact the sender by reply email and destroy al l copies of the original message. If you are the intended recipient, please be advised that the c ontent of this message is subject to access, review and disclosure by the sender's Email System A dministrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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] Fwd: converting to fsaverage space
Hi Doug -Using the overlay threshold flags, I see that the .mgh (yes, the .mg was a cut/paste typo) is in the occipital region and should be frontal, temporal and parietal regions. So, I must be doing something wrong in the mri_vol2surf command: mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii --out $SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mgh --srcreg $SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lhPlus - as the original ROI encompasses regions in both hemispheres (i.e., the left executive network has a region in the right cerebellum), I thought I would need to repeat this command with --hemi rh? I assumed I would have to runmris_aatomical_stats on each hemisphere -- after I have labels for the ROI for each hemisphere?Thanks,BarbaraThe vol2surf command outputshould be .mgh or .mgz, not .mg (or maybe that is just a typo in theemail). If it is, then you should load the mgh file as an overlay, notas a surface, egtksurfer [subj] lh inflated -overlay file.mgh -fminmax .5 1000setting the min threshold to .5 assures that you can see the ROIdougOn 03/13/2014 05:10 PM, Barbara Weiland wrote:Hi -Sorry to not have been clearer.I have /functional ROIs defined by the Greiciuslab// (http://findlab.stanford.edu/functional_ROIs.html) just as inthis post to the Freesurfer list from //Mon Dec 2 15:22:08 EST 2013:///Doug, Thank you for your very helpful suggestion. Indeed, doing somade it so I could quickly take any parts (or all) of each Greiciusnetwork and put them in individual subject space. In case this mayhelp anyone else, the final series of commands were (in this case,for the whole anterior salience network): *mni152reg --s [subj]*mri_label2vol *--seg anterior_Salience.nii.gz \* --reg$SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2mm.dat \ --invertmtx--o anterior_Salience_[subj].nii.gz \ --temp$SUBJECTS_DIR/[subj]/mri/orig.mgz Cheers, PaulThese ROIs were originally in MNI space and I used the commands listedabove from Paul to move them to subject space first creating thereg.mni152.2mm.dat for each subject. LECN….nii is one of thesenetwork ROIs. I can see this ROI using free view and it lookscorrect. What I want is to extract volume and thickness for this ROI.As outlined below,I thought I needed to first convert this to asurface and tried:mri_vol2surf --src $SUBJECTS_DIR/[subj]/label/LECN_subjXXX.nii --out$SUBJECTS_DIR/[subj]/label/LECN_subjXXX_lh_surf.mg --srcreg$SUBJECTS_DIR/[subj]/mri/transforms/reg.mni152.2.dat --hemi lhI tried to look at the output (LECN_subjXXX_lh_surf.mg) by usingtksurfer [subj] lh inflated and then load the it from the GUI onto theinflated surface -- this says that thefile (LECN_subjXXX_lh_surf.mg) "has 0 vertices!Probably trying to use a scalar data file as a surface!"Do I need to move the LECN….nii to be a surface or should I just beable to make a label from it? I assumed I need the ROI information tobe a label to use mris_anatomical_stats?Thank you,BarbaraBarbara Weiland, Ph.D.Research Asst. ProfessorCU Change LabDept. of Psychology NeuroscienceUniversity of Colorado Boulderbarbara.weil...@colorado.edu ___ 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] Extracting thickness, area and folding values from Qdec
Dear Doug, no, I did not put it in quotes. I just typed the mentioned command, but it is still not working. I can not find the file comprising the thickness, area or folding values at peak maxima after Monte Carlo simulation. Sorry for asking so many questions, but it is still not working. What should I do next? Best regards, DH Date: Thu, 13 Mar 2014 15:15:23 -0400 From: gr...@nmr.mgh.harvard.edu To: dusanhir...@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec are you puttting it in quotes? If so, don't doug On 03/13/2014 01:46 PM, Dusan Hirjak wrote: Dear Doug, I typed 1.3 but it is still not working. Any other ideas??? Thanks for your help. DH Date: Thu, 13 Mar 2014 12:20:57 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec Use 1.3 not 1,3 doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote: Dear Freesurfer Experts, I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster. I tried to run mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1,3 --sim-sign neg However, I got the ERROR: thresh = 1.3 not completely converted What am I doing wrong? Any other ideas? Is the pdf.dat file the right one to use??? Thanks! DH ___ 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. -- 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] Extracting thickness, area and folding values from Qdec
I think Doug meant the 1.3. Therefore the line should be something like: mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1.3 --sim-sign neg What exactly did you type? (try separating it with lines instead of quotes) HTH, D On Mar 13, 2014, at 6:22 PM, Dusan Hirjak wrote: Dear Doug, no, I did not put it in quotes. I just typed the mentioned command, but it is still not working. I can not find the file comprising the thickness, area or folding values at peak maxima after Monte Carlo simulation. Sorry for asking so many questions, but it is still not working. What should I do next? Best regards, DH Date: Thu, 13 Mar 2014 15:15:23 -0400 From: gr...@nmr.mgh.harvard.edu To: dusanhir...@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec are you puttting it in quotes? If so, don't doug On 03/13/2014 01:46 PM, Dusan Hirjak wrote: Dear Doug, I typed 1.3 but it is still not working. Any other ideas??? Thanks for your help. DH Date: Thu, 13 Mar 2014 12:20:57 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Extracting thickness, area and folding values from Qdec Use 1.3 not 1,3 doug On 03/13/2014 10:12 AM, Dusan Hirjak wrote: Dear Freesurfer Experts, I did a correlational analysis in qdec and found several significant clusters after Monte-Carlo simulation (0.05). Now, I would like to extract the mean cortical thickness, area and folding values (peak maximum) of each study subject above the significant cluster. I tried to run mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1,3 --sim-sign neg However, I got the ERROR: thresh = 1.3 not completely converted What am I doing wrong? Any other ideas? Is the pdf.dat file the right one to use??? Thanks! DH ___ 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. -- 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
Re: [Freesurfer] Running Tracula on a cluster
Hello, I recently modified my script so that it would work on a cluster. I had been running it successfully locally but am now having some trouble on the cluster. The only thing I changed in the dmrirc script were some pathways. However, I keep getting an error of must specify as many dicoms as subjects. I did not change any dicom numbers in this once successfully working script. Attached is my script. Any thoughts? Thanks, Emily - Original Message - From: ebell...@uwm.edu To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:25:00 PM Subject: Re: [Freesurfer] Running Tracula on a cluster Hi Anastasia, We use SLURM. I have not personally yet run bedpost off of the cluster, but one of my colleagues was able to run his data off of our cluster ( the whole pathway including bedpost) without any problem. However he (Jon Wieser) made an individual dmrirc configuration file script for every subject and then made sure each one got assigned to a different processor in another script. Thanks, Emily - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: ebell...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:02:14 PM Subject: Re: [Freesurfer] Running Tracula on a cluster Hi Emily - Which job management system does your cluster run on? Have you ever tried to run any of the FSL parallelized programs, like bedpostx, on your cluster? a.y On Wed, 5 Mar 2014, ebell...@uwm.edu wrote: Hello, I plan on running a batch of subjects (around 80) on a computer cluster. I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist? However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster? I have attached my dmrirc file as well as the files needed for it to run on the cluster. Thanks, Emily 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. dmrirc.example_final Description: Binary data ___ 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] Running Tracula on a cluster
Hi Emily - Replace sub238/DTI/i*.MRDC.1 with a single file name. a.y On Thu, 13 Mar 2014, ebell...@uwm.edu wrote: Hello, I recently modified my script so that it would work on a cluster. I had been running it successfully locally but am now having some trouble on the cluster. The only thing I changed in the dmrirc script were some pathways. However, I keep getting an error of must specify as many dicoms as subjects. I did not change any dicom numbers in this once successfully working script. Attached is my script. Any thoughts? Thanks, Emily - Original Message - From: ebell...@uwm.edu To: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:25:00 PM Subject: Re: [Freesurfer] Running Tracula on a cluster Hi Anastasia, We use SLURM. I have not personally yet run bedpost off of the cluster, but one of my colleagues was able to run his data off of our cluster ( the whole pathway including bedpost) without any problem. However he (Jon Wieser) made an individual dmrirc configuration file script for every subject and then made sure each one got assigned to a different processor in another script. Thanks, Emily - Original Message - From: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu To: ebell...@uwm.edu Cc: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 5, 2014 3:02:14 PM Subject: Re: [Freesurfer] Running Tracula on a cluster Hi Emily - Which job management system does your cluster run on? Have you ever tried to run any of the FSL parallelized programs, like bedpostx, on your cluster? a.y On Wed, 5 Mar 2014, ebell...@uwm.edu wrote: Hello, I plan on running a batch of subjects (around 80) on a computer cluster. I am assuming that in the dmrirc configuration file, I can enter all of the subjects in subjlist? However, do I have to add something to it to make sure that each subject gets sent to a different processor on the cluster? I have attached my dmrirc file as well as the files needed for it to run on the cluster. Thanks, Emily 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
[Freesurfer] freeview bug
hi freesurfer folks, just had a nasty bug crash my whole mac workstation. yikes! i loaded lh and rh pial surfaces into freeview and went to assign annotation files to each and when i did i inadvertantly (aka randomly) selected the wrong file in labels dir- a .csv file i believe - instead of throwing an error dialogue with an appropriately snarky message it brought my whole system down, protected memory and all. never seen that before. after automatic reboot all was fine but this one is nasty. all current work was lost. hw was std mac pro osx 10.7.5, 96 GB mem. jeff ___ 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.
