Re: [Freesurfer] treatment effect compare to controls
Hi Martin, Thanks for your instructions. In my analysis when we look at Two Stage Model results within our control group , we see increase in thickness (thickening) more than decrease (thinning), where we expect to see the thinning effect. Is there any explanation for this? I have 19 controls with 2 to 3 years difference between tp1 and tp2. Best regards, Amirhossein Manzouri On Mon, Feb 23, 2015 at 5:25 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi, yes, the first is to stack all the data into a single file (on your study average, usually that is fsaverage). The second steps smoothes the data. You can use different smoothing levels, depending on your data. Usually 10 or 15 is a good number. The data will automatically be taken from the sub1t1.long.tempsub1 etc directories (this is signaled by the --qdec-long flag. The qdec table needs to be in the longitudinal format, that means the first column is the subject id (sub1-t1) the second column the base name (tempsub1) column headers are fsid fsid-base …. usually the third column is time from baseline (in years), but can be any time variable that you want to use in the LME. There is an example of the longitudinal qdec table here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel I'll probably add that to the lme page so it is easier to find. Best, Martin On Feb 23, 2015, at 4:54 AM, amirhossein manzouri a.h.manzo...@gmail.com wrote: Hi and thanks Martin for your help, I am trying to do mixed effect analysis, should I use the registered to template data for this ( sub1-t1.long.tempsub1 and sub1-t2.long.tempsub1) and how should the aded.table.dat look like? Do I need to run : mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh --meas thickness --out lh.thickness.mgh mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu 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] multiple comparisons correction for individual hemispheres (native space)
Hi Antonin, please remember to send responses to the list. Thanks! I've put a new version of cluster-sess in that same location. Let me know if that works. for the mri_mcsim command, make sure to pass it a fwhm that is an integer. Also, I would probably just run it with --fwhm-max so that it does all the fwhms below the max. There is virtually no time penalty for this and it may be useful in other cases where the fwhm is not exactly the same. doug On 03/03/2015 08:42 AM, Antonin Skoch wrote: Dear Douglas, thank you very much for the file. It seems, that the -cache-dir parameter is not parsed properly in this script. By -cache-dir you fill-in the CacheDir variable, but it is never used and at line 182 you use for csd directory construction variable SimDir which hard-coded points to $SUBJECTS_DIR/fsaverage/mult-comp-cor. But when I corrected for this, it works in principle. Could you please check that I understand the usage correctly? I simulated my own distribution in subject's native space by using mri_mcsim, for example for right hemisphere by this command mri_mcsim --o subject_name/rh/cortex --base mc-z --surf subject_name rh --nreps 1 --fwhm my_fwhm(from fwhm.dat in analysis directory) and then run cluster-sess -analysis analysis_name -thresh 2 -a2009s -2spaces -cache-dir dir_of_my_simulation -s session_ID Regards, Antonin *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] *To:* Antonin Skoch [mailto:a...@medicon.cz] *Sent:* Mon, 02 Mar 2015 21:07:36 +0100 *Subject:* Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Sorry, try it now On 03/02/2015 02:42 PM, Antonin Skoch wrote: Dear Douglas, I am also interested in multiple comparisons correction in first-level analysis for individual hemispheres in fsFast. Unfortunately, your file ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess which you provided for Christopher in November 2014 is not available at that location. Could you please provide this file permanently for other users? Regards, Antonin Skoch Institute for Clinical and Experimental Medicine Czech Republic -- 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/ 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] QDEC longitudinal analysis
Hi Carolina, the command long_qdec_table reduces your longitudinal table (the one with the second column 'fsid-base') into cross sectional format with one line per subject. That's all it does. In order to create the within-subject rate and percent change maps, you need to run long_mris_slopes first. That will create a within subject rate map (via a linear fit into the longitudinal data within each subject) and map the results to the study template (usually fsaverage), it also performs smoothing. You are right that, in order to run the cross sectional analysis of rate-maps with QDEC you would need to modify the qdecrc Documentation can be found here: http://freesurfer.net/fswiki/LongitudinalTwoStageModel Note that we recommend to use Linear Mixed Effects models for analysis of longitudinal data (which currently requires matlab): http://freesurfer.net/fswiki/LinearMixedEffectsModels Best, Martin On Mar 3, 2015, at 2:46 AM, carolina.mr carolina...@uol.com.br wrote: Hello Freesurfers, I am trying to run QDEC for a longitudinal analysis. I've run the command long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat to adjust my qdec table to the right format for QDEC (with only one line / subject). I've also created the .Qdecrc file in my qdec directory. But, my end up table contains the fsid with my base images. When I run the analysis, appears an error message: Error in analyze: Couldn't open /baseID/surf/lh.thickness.fwhm10.fsaverage.mgz file. Indeed, this file does not exist in the base directory (but I think it was not supposed to be there). Additionaly, I was interested in test the correlation between spc and rate and the changes in the clinical parameters of my sample. I though it would be feasible after creating .Qdecrc file. Is that right? Kind regards, Carolina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.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] equivalent for fslmaths -mas option in freesurfer
The command I used to visualise the label converted to volume form (using
mri_label2vol) in tkmedit was
tkmedit V2_subject5_1 orig.mgz -overlay V2_lh.mgz -overlay-reg register.dat
-fthresh .5 -fmid 1
my tksurfer command was
tksurfer V2_subject5_1 lh inflated
where I then attempted to overlay V2_lh.mgz as an overlay using the
register.dat file to register. This produces no visible overlay.
I have just retried with fill thresh set to 0 but no change to whether any data
is visible on the inflated surface.
V2_colour_lh.mgz is the functional overlay that I want to extract any data
active within V2 from, this was produced by my usage of mri_vol2surf
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {V2_colour_lh} --out_type {mgz}
essentially what I wanted was to take mask a functional volume of colour
activation across the occipital cortex with a V2 mask to only see activation
within V2 on the inflated surface.
I have a V2.label file and a V2_colour_lh.mgz file overlaid onto an inflated
surface using mri_vol2surf.
thanks
S
From: Sarah Finnegan
Sent: 03 March 2015 14:41
To: Freesurfer support list
Subject: RE: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Doug,
Thanks I had hoped to use mri_mask but was foiled in my attempt to convert the
.label files to .mgz using mri_label2bvol. I assumed I must be on the wrong
track.
my command was
mri_label2vol --label V2_lh.label --temp f.nii.gz --reg register.dat
--fillthresh .3 --proj frac 0 1 .1 --subject V2_subject5 --hemi lh --o V2_lh.mgz
I have previously used this command successfully to convert labels for usage in
FSL. The volume will display using tkmedit on the orig surface, but in tksurfer
using the inflated surface there is nothing visible when attempting to open as
an overlay.
I have played around with different options and attempted to move forward to
mri_mask using the V2_lh.mgz file (hoping to later open the data in tksurfer)
but the command
mri_mask -transfer 255 -keep_mask_deletion_edits masked_data V2_lh.mgz
lh_colour.mgz V2_colour_lh.mgz
gives
transfer mask voxels=255 to dst vol
Transferring mask edits ('1' voxels) to dst vol
ERROR: dimension mismatch between source and mask
I assume I must be missing something fundamental in the mri_label2vol command?
Thank you for your help
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sarah Finnegan
[sarah.finne...@stcatz.ox.ac.uk]
Sent: 26 February 2015 15:12
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Bruce
Thanks for your reply,
I did use mri_vol2surf for the sampling
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {out file name} --out_type {mgz}
I don't believe that I want to average within the ROI. I want to take any
clusters of activity within V2 and feed this into a script i'm developing in
MATLAB to work out the distance between different voxel clusters and the size
of each cluster, but only for within my region defined as V2. Hopefully that
makes sense, If I average I think I will lose this spatial information?
Thanks
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 26 February 2015 15:04
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Sarah
have you used mri_vol2surf to sample the data onto the surface? When you
say extract specific regions of functional data from a flat do you
want to average within the ROI?
cheers
Bruce
On Thu, 26 Feb 2015, Sarah Finnegan wrote:
I have a question about the equivalent of fslmaths -mas option in
freesurfer.
I have several manually defined labels in .label form that I want to use to
extract specific regions of functional data from a flat patch. Ordinarily in
fsl I would just use
fslmaths -invol {functional_data} -mas {bin_label} -outvol
{masked_functional_data}
but I'm a little confused about an equivalent for this in free surfer as I
don't want to perform any further stats on these ROI yet, extract them from
any surrounding data and overlay onto the flattened surface.
I have tried using
mri_vol2roi --label {V2_rh.label} --srcvol {functional_data.mgz} --srcreg
{anat2exf.register.dat} --roiavg {func_V2_mask} --finalmskvol
{func_V2_mask_out}
but when overlaying the output file there are no data points visible.
Any help would be great as several other functions that I have tried seem to
be obsolete,
Thanks!
Sarah
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
I don't know, esp since it is an approximation to begin with. An alternative is to take the offsets from your multi-time-point subjects and the single maps from your subjects with one time point and run that through the one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then you should subtract the mean age of the one time-point subjects from the age of the multi-time point subjects before the 1st stage of analysis. doug On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote: Hi Doug, thank you very much for your answer! Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: You would do the long analysis using a random effects analysis. OK, so basically do 2-stage modeling (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right? For each subject you can get a slope (this won't work if the subject only has 1 time point), then concatenate the slopes into a file and run mri_glmfit, then follow the procedures from the archive email you reference. One quarter of my subjects only has one measurement time point. Can I still use this method (which would only consider the 3/4 of the subjects) to correct clusters found in the whole group? Or would it only be valid for correcting clusters from an LME model for the reduced group? Thanks, Janosch doug On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote: Hi Doug and others, I would like apply (Monte Carlo simulation) cluster correction (as opposed to the implemented vertex-wise FDR correction) on the results from a longitudinal study I analyzed using the LME toolbox. The design is unbalanced (different number of time points, from 1 to 4, per subject). In this thread (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) you, Doug, suggested, if I understand correctly: - concatenating the images using `mris_preproc --paired-diff` - smooth with the same kernel size as used in the lme analysis - running `mri_glmfit` on them with an fsgd file that uses the same covariates and the same contrast (excluding the interaction term with time) as used in the lme analysis - overwriting sig.mgh with the one from the lme analysis - running `mri_glmfit-sim --cache` How would I extend this to my case where I don't have pairwise images, but 1 image for some participants, for others up to 4? Thanks a lot, Janosch -- 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/ 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
[Freesurfer] Mapping Own DK Regional Stats onto Surface
Hi all, I’d like to map my own stats (one value per Desikan-Killiany region) onto a subject's surface file, to create a figure similar to the following: http://openi.nlm.nih.gov/detailedresult.php?img=3280212_pone.0031913.g001req=4 To do this, I tried to create a scalar overlay file using mris_convert’s --parcstats option, per the following mris_convert example: “” Create a scalar overlay file where each parcellation region contains a single value: mris_convert \ --annot lh.aparc.annot \ --parcstats lh.parcstats.txt \ lh.white \ lh.parcstats (...) --parcstats infile is the name of text file containing label/val pairs, where label is an annot name and val is a value associated with that label. “” However, looking at the output file, stats didn’t seem to map to any vertices; instead, I observed zeroes across all in both Freeview and after conversion to ASCII (see first few lines below). I tried a few other ways to delimit the “label/val” pairs of the --parcstats file, including using tab, space, and forward-slash, but each way seemed to produce the same results: 000 -10.67346 -71.19921 6.09064 0.0 001 -11.29567 -71.20504 6.32133 0.0 002 -12.26970 -71.62605 6.00416 0.0 003 -13.11823 -71.40913 6.45834 0.0 004 -14.22002 -71.39742 6.28750 0.0 So, I wonder: is using mris_convert with the --parcstats flag a correct way to create such a map? If so, what could have gone wrong? If not, what’s the easiest way to map my own regional stats onto a surface? Your expertise is greatly appreciated; Thanks and all the best, Tony Jin Data Technician Dept. of Psychiatry Stony Brook Medicine This e-mail message, including any attachments, 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 e-mail and destroy all copies of the original. ___ 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] equivalent for fslmaths -mas option in freesurfer
On 03/03/2015 10:43 AM, Sarah Finnegan wrote:
The command I used to visualise the label converted to volume form (using
mri_label2vol) in tkmedit was
tkmedit V2_subject5_1 orig.mgz -overlay V2_lh.mgz -overlay-reg
register.dat -fthresh .5 -fmid 1
my tksurfer command was
tksurfer V2_subject5_1 lh inflated
where I then attempted to overlay V2_lh.mgz as an overlay using the
register.dat file to register. This produces no visible overlay.
This does not surprise me too much. The mask will be very thin and
you'll have to make sure to sample it properly. So, try running
mri_vol2surf with V2_lh.mgz as the input and a projection fraction of
0.5. Then load the result as an overlay in tksurfer, eg,
tksurfer V2_subject5_1 lh inflated -overlay yournewfile.mgz -fminmax 0.5 1
I have just retried with fill thresh set to 0 but no change to whether any
data is visible on the inflated surface.
V2_colour_lh.mgz is the functional overlay that I want to extract any data
active within V2 from, this was produced by my usage of mri_vol2surf
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {V2_colour_lh} --out_type {mgz}
essentially what I wanted was to take mask a functional volume of colour
activation across the occipital cortex with a V2 mask to only see activation
within V2 on the inflated surface.
I have a V2.label file and a V2_colour_lh.mgz file overlaid onto an inflated
surface using mri_vol2surf.
You'll need to decide what space you want to do the masking in. The way
you have it now, you have the mask in volume space and the thing to be
masked in surface space (thus the dimension error).
doug
thanks
S
From: Sarah Finnegan
Sent: 03 March 2015 14:41
To: Freesurfer support list
Subject: RE: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Doug,
Thanks I had hoped to use mri_mask but was foiled in my attempt to convert
the .label files to .mgz using mri_label2bvol. I assumed I must be on the
wrong track.
my command was
mri_label2vol --label V2_lh.label --temp f.nii.gz --reg register.dat
--fillthresh .3 --proj frac 0 1 .1 --subject V2_subject5 --hemi lh --o
V2_lh.mgz
I have previously used this command successfully to convert labels for usage
in FSL. The volume will display using tkmedit on the orig surface, but in
tksurfer using the inflated surface there is nothing visible when attempting
to open as an overlay.
I have played around with different options and attempted to move forward to
mri_mask using the V2_lh.mgz file (hoping to later open the data in tksurfer)
but the command
mri_mask -transfer 255 -keep_mask_deletion_edits masked_data V2_lh.mgz
lh_colour.mgz V2_colour_lh.mgz
gives
transfer mask voxels=255 to dst vol
Transferring mask edits ('1' voxels) to dst vol
ERROR: dimension mismatch between source and mask
I assume I must be missing something fundamental in the mri_label2vol command?
Thank you for your help
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sarah Finnegan
[sarah.finne...@stcatz.ox.ac.uk]
Sent: 26 February 2015 15:12
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Bruce
Thanks for your reply,
I did use mri_vol2surf for the sampling
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {out file name} --out_type {mgz}
I don't believe that I want to average within the ROI. I want to take any
clusters of activity within V2 and feed this into a script i'm developing in
MATLAB to work out the distance between different voxel clusters and the size
of each cluster, but only for within my region defined as V2. Hopefully that
makes sense, If I average I think I will lose this spatial information?
Thanks
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 26 February 2015 15:04
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Sarah
have you used mri_vol2surf to sample the data onto the surface? When you
say extract specific regions of functional data from a flat do you
want to average within the ROI?
cheers
Bruce
On Thu, 26 Feb 2015, Sarah Finnegan wrote:
I have a question about the equivalent of fslmaths -mas option in
freesurfer.
I have several manually defined labels in .label form that I want to use to
extract specific regions of functional data from a flat patch. Ordinarily in
fsl I would just use
fslmaths -invol {functional_data} -mas {bin_label} -outvol
{masked_functional_data}
but I'm a little confused about an equivalent for this in free
Re: [Freesurfer] Bad design matrix
I think just using DOSS instead of DODS will do it (--fsgd your.fsgd doss) On 03/03/2015 12:42 AM, Anders Hougaard wrote: Thanks Doug. Any suggestions for a more appropriate design? I guess this is a common situation where two or more parameters only apply to one group (in this case patients) and are zero or constant in the other. Best, Anders 2015-03-02 21:21 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: It looks like the 4th column is always -0.9 and the 6th col is always -9.138 which makes them redundant with column 2 and causes the error. doug On 03/02/2015 03:16 PM, Anders Hougaard wrote: Dear Doug, Thanks for the answer. I deliberately chose not to demean. With demeaning I get the same error (see below). Any suggestions? Best, Anders Design matrix -- 1.000 0.000 -0.600 0.000 17.137 0.000; 1.000 0.000 -0.800 0.000 11.962 0.000; 1.000 0.000 7.100 0.000 11.190 0.000; 1.000 0.000 0.700 0.000 30.736 0.000; 1.000 0.000 3.100 0.000 23.735 0.000; 1.000 0.000 0.100 0.000 21.121 0.000; 1.000 0.000 1.100 0.000 12.395 0.000; 1.000 0.000 2.100 0.000 24.912 0.000; 1.000 0.000 0.100 0.000 -8.021 0.000; 1.000 0.000 -0.700 0.000 8.877 0.000; 1.000 0.000 0.100 0.000 0.893 0.000; 1.000 0.000 7.100 0.000 29.849 0.000; 1.000 0.000 -0.400 0.000 -1.825 0.000; 1.000 0.000 2.100 0.000 14.361 0.000; 1.000 0.000 2.100 0.000 7.267 0.000; 1.000 0.000 0.100 0.000 34.169 0.000; 1.000 0.000 0.100 0.000 30.500 0.000; 1.000 0.000 1.100 0.000 9.219 0.000; 1.000 0.000 0.100 0.000 26.270 0.000; 1.000 0.000 1.100 0.000 2.320 0.000; 1.000 0.000 0.100 0.000 22.325 0.000; 1.000 0.000 0.100 0.000 13.323 0.000; 1.000 0.000 1.100 0.000 -2.628 0.000; 1.000 0.000 7.100 0.000 12.379 0.000; 1.000 0.000 1.100 0.000 -2.581 0.000; 1.000 0.000 0.100 0.000 -4.492 0.000; 1.000 0.000 1.100 0.000 11.549 0.000; 1.000 0.000 0.100 0.000 -8.413 0.000; 1.000 0.000 1.100 0.000 9.663 0.000; 1.000 0.000 1.100 0.000 8.655 0.000; 1.000 0.000 1.100 0.000 25.778 0.000; 1.000 0.000 3.100 0.000 2.739 0.000; 1.000 0.000 0.100 0.000 21.745 0.000; 1.000 0.000 -0.400 0.000 -5.762 0.000; 1.000 0.000 0.100 0.000 14.969 0.000; 1.000 0.000 0.100 0.000 3.535 0.000; 1.000 0.000 0.100 0.000 -0.287 0.000; 1.000 0.000 1.100 0.000 -2.283 0.000; 1.000 0.000 0.100 0.000 -0.257 0.000; 1.000 0.000 0.100 0.000 -1.207 0.000; 1.000 0.000 0.100 0.000 1.140 0.000; 1.000 0.000 0.600 0.000 -4.829 0.000; 1.000 0.000 1.100 0.000 2.213 0.000; 1.000 0.000 0.100 0.000 2.503 0.000; 1.000 0.000 0.600 0.000 3.193 0.000; 1.000 0.000 0.100 0.000 10.361 0.000; 1.000 0.000 0.100 0.000 3.546 0.000; 1.000 0.000 6.600 0.000 12.532 0.000; 1.000 0.000 0.100 0.000 -1.286 0.000; 1.000 0.000 0.100 0.000 -5.428 0.000; 1.000 0.000 -0.400 0.000 -1.661 0.000; 1.000 0.000 -0.800 0.000 21.444 0.000; 1.000 0.000 0.100 0.000 21.517 0.000; 1.000 0.000 -0.600 0.000 8.515 0.000; 1.000 0.000 0.100 0.000 19.530 0.000; 1.000 0.000 1.100 0.000 1.824 0.000; 1.000 0.000 0.100 0.000 15.795 0.000; 1.000 0.000 0.600 0.000 -6.140 0.000; 1.000 0.000 2.600 0.000 0.803 0.000; 1.000 0.000 0.100 0.000 16.904 0.000; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000 0.000 -0.900 0.000 -9.138; 0.000 1.000
Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface
That is the right way (or one of them). Did you look at the result in tksurfer? On 03/03/2015 11:34 AM, Jin, Tony wrote: Hi all, I’d like to map my own stats (one value per Desikan-Killiany region) onto a subject's surface file, to create a figure similar to the following: http://openi.nlm.nih.gov/detailedresult.php?img=3280212_pone.0031913.g001req=4 To do this, I tried to create a scalar overlay file using mris_convert’s --parcstats option, per the following mris_convert example: “” Create a scalar overlay file where each parcellation region contains a single value: mris_convert \ --annot lh.aparc.annot \ --parcstats lh.parcstats.txt \ lh.white \ lh.parcstats (...) --parcstats infile is the name of text file containing label/val pairs, where label is an annot name and val is a value associated with that label. “” However, looking at the output file, stats didn’t seem to map to any vertices; instead, I observed zeroes across all in both Freeview and after conversion to ASCII (see first few lines below). I tried a few other ways to delimit the “label/val” pairs of the --parcstats file, including using tab, space, and forward-slash, but each way seemed to produce the same results: 000 -10.67346 -71.19921 6.09064 0.0 001 -11.29567 -71.20504 6.32133 0.0 002 -12.26970 -71.62605 6.00416 0.0 003 -13.11823 -71.40913 6.45834 0.0 004 -14.22002 -71.39742 6.28750 0.0 So, I wonder: is using mris_convert with the --parcstats flag a correct way to create such a map? If so, what could have gone wrong? If not, what’s the easiest way to map my own regional stats onto a surface? Your expertise is greatly appreciated; Thanks and all the best, Tony Jin Data Technician Dept. of Psychiatry Stony Brook Medicine This e-mail message, including any attachments, 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 e-mail and destroy all copies of the original. ___ 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] equivalent for fslmaths -mas option in freesurfer
Hi Doug,
Thanks! the combination of sampling incorrectly and confusion of spaces was the
root of the problem.
Everything is now looking as it should.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: 03 March 2015 16:00
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
On 03/03/2015 10:43 AM, Sarah Finnegan wrote:
The command I used to visualise the label converted to volume form (using
mri_label2vol) in tkmedit was
tkmedit V2_subject5_1 orig.mgz -overlay V2_lh.mgz -overlay-reg
register.dat -fthresh .5 -fmid 1
my tksurfer command was
tksurfer V2_subject5_1 lh inflated
where I then attempted to overlay V2_lh.mgz as an overlay using the
register.dat file to register. This produces no visible overlay.
This does not surprise me too much. The mask will be very thin and
you'll have to make sure to sample it properly. So, try running
mri_vol2surf with V2_lh.mgz as the input and a projection fraction of
0.5. Then load the result as an overlay in tksurfer, eg,
tksurfer V2_subject5_1 lh inflated -overlay yournewfile.mgz -fminmax 0.5 1
I have just retried with fill thresh set to 0 but no change to whether any
data is visible on the inflated surface.
V2_colour_lh.mgz is the functional overlay that I want to extract any data
active within V2 from, this was produced by my usage of mri_vol2surf
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {V2_colour_lh} --out_type {mgz}
essentially what I wanted was to take mask a functional volume of colour
activation across the occipital cortex with a V2 mask to only see activation
within V2 on the inflated surface.
I have a V2.label file and a V2_colour_lh.mgz file overlaid onto an inflated
surface using mri_vol2surf.
You'll need to decide what space you want to do the masking in. The way
you have it now, you have the mask in volume space and the thing to be
masked in surface space (thus the dimension error).
doug
thanks
S
From: Sarah Finnegan
Sent: 03 March 2015 14:41
To: Freesurfer support list
Subject: RE: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Doug,
Thanks I had hoped to use mri_mask but was foiled in my attempt to convert
the .label files to .mgz using mri_label2bvol. I assumed I must be on the
wrong track.
my command was
mri_label2vol --label V2_lh.label --temp f.nii.gz --reg register.dat
--fillthresh .3 --proj frac 0 1 .1 --subject V2_subject5 --hemi lh --o
V2_lh.mgz
I have previously used this command successfully to convert labels for usage
in FSL. The volume will display using tkmedit on the orig surface, but in
tksurfer using the inflated surface there is nothing visible when attempting
to open as an overlay.
I have played around with different options and attempted to move forward to
mri_mask using the V2_lh.mgz file (hoping to later open the data in tksurfer)
but the command
mri_mask -transfer 255 -keep_mask_deletion_edits masked_data V2_lh.mgz
lh_colour.mgz V2_colour_lh.mgz
gives
transfer mask voxels=255 to dst vol
Transferring mask edits ('1' voxels) to dst vol
ERROR: dimension mismatch between source and mask
I assume I must be missing something fundamental in the mri_label2vol command?
Thank you for your help
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sarah Finnegan
[sarah.finne...@stcatz.ox.ac.uk]
Sent: 26 February 2015 15:12
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Bruce
Thanks for your reply,
I did use mri_vol2surf for the sampling
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {out file name} --out_type {mgz}
I don't believe that I want to average within the ROI. I want to take any
clusters of activity within V2 and feed this into a script i'm developing in
MATLAB to work out the distance between different voxel clusters and the size
of each cluster, but only for within my region defined as V2. Hopefully that
makes sense, If I average I think I will lose this spatial information?
Thanks
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 26 February 2015 15:04
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Sarah
have you used mri_vol2surf to sample the data onto the surface? When you
say extract specific regions of functional data from a flat do you
want to average within the ROI?
Re: [Freesurfer] lGI ?h.pial-outer-smoothed
Hi Giedre, Small intersections like that are fine and won't affect the lGI computation, so you are good with that. Values around 20 are however more preoccupying! Can you send me a screenshot of the lGI overlaid on the surface for this subject using tksurfer or freeview? Best, Marie NB: if you are interested in thickness as well, you might want to correct the segmentation in the parahippocampal gyrus for this subject (the drop-shaped WM inclusion in the cortex). On Mar 3, 2015, at 6:58 AM, Stripeikyte, G. g.stripeik...@umcutrecht.nlmailto:g.stripeik...@umcutrecht.nl wrote: Dear freesurfers, I am analysing localGI and noticed that sometimes scans with ?h.pial-outer-smoothed surface intersect ?h.pial surface (attached pic.). Is this normal or should I correct parameters and rerun localGI? Also when I extracted ROI lGI values I got some extremely high results. For example in lh_insula and rh_insula, for some participants lGI reach about 20. Scans look normal of these participants. Are such high values possible or something wrong with calculation? Sincerely, Giedre De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail. pial-outer-smoothed.png___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] from vol timecourse to surf timecourse
Dear Surfer experts, (Most likely Dough) It is common practice to perform the slice time correction first and than the motion correction. However free surfer seems to work in the opposite way. I have tried to write a mini matlab freesurfer script for the common way. system([stc-sess -s funcdir(i).name -i f -o fstc -so siemens]) system([mc-sess -s funcdir(i).name -fstem fstc -fmcstem fstcmc -per-run]) This seems to work. My problem is how do I get the resulting fstcmc.ni.gz on to the fsaverage surface using spherical alignment? Jan ___ 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] Tracula: cannot open file `1000' for reading Bedpost file error
Hello Freesurfers, I recently updated my Freesurfer version and now I am getting an error in tracula. awk: cmd. line:1: fatal: cannot open file `1000' for reading (No such file or directory) Any help would be appreciated. trac-all.error Description: Binary data Mon Mar 2 18:24:56 CST 2015 /home/k/ksd770/Desktop/Subj/090 /usr/local/freesurfer/bin/trac-all -prep -c 090.dmrirc Subject 090 SUBJECTS_DIR /home/k/ksd770/Desktop/Subj FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-504.8.1.el6.x86_64 #1 SMP Fri Dec 19 12:09:25 EST 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 126968 total used free sharedbuffers cached Mem: 16275144 103039725971172 12916 896047644376 -/+ buffers/cache:2569992 13705152 Swap: 8208380 748248133556 Program versions: $Id: trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/03-00:24:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/03-00:24:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/03-00:24:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/03-00:24:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/03-00:24:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: User: root Machine: kate.ad.wcas.northwestern.edu Platform: Linux PlatformVersion: 2.6.32-504.8.1.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /projects/p20394/software/freesurfer-v5.3.0 New invocation of trac-preproc root kate.ad.wcas.northwestern.edu Linux kate.ad.wcas.northwestern.edu 2.6.32-504.8.1.el6.x86_64 #1 SMP Fri Dec 19 12:09:25 EST 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize10240 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 126968 total used free sharedbuffers cached Mem: 16275144 103163885958756 12916 896047644376 -/+ buffers/cache:2582408 13692736 Swap: 8208380 748248133556 #- /usr/local/freesurfer/bin/trac-preproc #- #@# Image corrections Mon Mar 2 18:24:57 CST 2015 mri_convert /home/k/ksd770/Desktop/Subj/090/orig/90.MR.FMRI_STUDIES_NUSSLOCK.6.1.20140620.100913.pmv751.dcm /home/k/ksd770/Desktop/Subj/090/dmri/dwi_orig.nii.gz mri_convert /home/k/ksd770/Desktop/Subj/090/orig/90.MR.FMRI_STUDIES_NUSSLOCK.6.1.20140620.100913.pmv751.dcm /home/k/ksd770/Desktop/Subj/090/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/k/ksd770/Desktop/Subj/090/orig/90.MR.FMRI_STUDIES_NUSSLOCK.6.1.20140620.100913.pmv751.dcm... Getting Series No INFO: Found 67 files in /home/k/ksd770/Desktop/Subj/090/orig INFO: Scanning for Series Number 6 Scanning Directory INFO: found 65 files in series INFO: loading series header info. RunNo = 5 WARNING: Run 1 appears to be truncated Files Found: 65, Files Expected (lRep+1): 1 FileName
[Freesurfer] Fwd: Recon-all Error
HI, Im using freesurfer newly, i have a folder of a subject's MRI's named 139942 I tried to run recon-all of a File named I000 The point is to get Superior temporal gyrus thickness. but it show an error and stop working. i looked up archive of FAQ's but i didnt anything usefull. There is the recon-all log attached! Please Help! By the way I'm using Ubuntu 14.04 LTS!! چهارشنبه ۰۴ مارس ۱۵، ساعت ۰۹:۴۷:۱۵ (IRST) /usr/local/freesurfer/subjects/139942 /usr/local/freesurfer/bin/recon-all -s 139942 -i /usr/local/139942/I000 subjid 139942 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux circle-Ubuntu 3.13.0-32-generic #57-Ubuntu SMP Tue Jul 15 03:51:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 47440 maxlocks unlimited maxsignal47440 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 609403227211923372840 24664 1398361525816 -/+ buffers/cache:10555405038492 Swap: 102396 0 102396 program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-06:17:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-06:17:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-06:17:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-06:17:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-06:17:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-06:17:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-06:17:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/03/04-06:17:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: root Machine: circle-Ubuntu Platform: Linux PlatformVersion: 3.13.0-32-generic CompilerName: GCC CompilerVersion: 40400 === NUMBER OF OPENMP THREADS = 1 === ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp:
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Am 03.03.2015 um 14:42 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: Some of this Martin will have to comment on, but my comments below On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote: Hey Doug, thanks again! That means, I would do something like: 1.) construct longitudinal qdec table - only use fsid, fsid-base, and years/age columns - substract the average age of the one-time point subjects from years/age value for every subject at every time point 2.) run long_mris_slopes - use the --do-avg flag? Yes, I think so 3.) concatenate the output files from 2) and the maps from the one-time point subjects with mris_preproc - use --is flag to select maps by specifying full path What command are you talking about to do the concatenation? mris_preproc, I thought. Thanks for your help, Janosch Otherwise sounds right. Make sure you use the average of the time points from long_mris_slopes and not the slope. 4.) run mri_glmfit - use --osgm flag for one-sample group mean Yes 5.) replace sig.mgz file with the one from LME analysis and run mri_glmfit-sim Yes Is that correct? (especially, is using --do-avg what you meant by taking the offset) Thanks, Janosch Am 03.03.2015 um 08:32 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: I don't know, esp since it is an approximation to begin with. An alternative is to take the offsets from your multi-time-point subjects and the single maps from your subjects with one time point and run that through the one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then you should subtract the mean age of the one time-point subjects from the age of the multi-time point subjects before the 1st stage of analysis. doug On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote: Hi Doug, thank you very much for your answer! Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: You would do the long analysis using a random effects analysis. OK, so basically do 2-stage modeling (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right? For each subject you can get a slope (this won't work if the subject only has 1 time point), then concatenate the slopes into a file and run mri_glmfit, then follow the procedures from the archive email you reference. One quarter of my subjects only has one measurement time point. Can I still use this method (which would only consider the 3/4 of the subjects) to correct clusters found in the whole group? Or would it only be valid for correcting clusters from an LME model for the reduced group? Thanks, Janosch doug On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote: Hi Doug and others, I would like apply (Monte Carlo simulation) cluster correction (as opposed to the implemented vertex-wise FDR correction) on the results from a longitudinal study I analyzed using the LME toolbox. The design is unbalanced (different number of time points, from 1 to 4, per subject). In this thread (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) you, Doug, suggested, if I understand correctly: - concatenating the images using `mris_preproc --paired-diff` - smooth with the same kernel size as used in the lme analysis - running `mri_glmfit` on them with an fsgd file that uses the same covariates and the same contrast (excluding the interaction term with time) as used in the lme analysis - overwriting sig.mgh with the one from the lme analysis - running `mri_glmfit-sim --cache` How would I extend this to my case where I don't have pairwise images, but 1 image for some participants, for others up to 4? Thanks a lot, Janosch -- 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/ 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/ -- Douglas N. Greve, Ph.D. MGH-NMR Center
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Some of this Martin will have to comment on, but my comments below On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote: Hey Doug, thanks again! That means, I would do something like: 1.) construct longitudinal qdec table - only use fsid, fsid-base, and years/age columns - substract the average age of the one-time point subjects from years/age value for every subject at every time point 2.) run long_mris_slopes - use the --do-avg flag? Yes, I think so 3.) concatenate the output files from 2) and the maps from the one-time point subjects with mris_preproc - use --is flag to select maps by specifying full path What command are you talking about to do the concatenation? Otherwise sounds right. Make sure you use the average of the time points from long_mris_slopes and not the slope. 4.) run mri_glmfit - use --osgm flag for one-sample group mean Yes 5.) replace sig.mgz file with the one from LME analysis and run mri_glmfit-sim Yes Is that correct? (especially, is using --do-avg what you meant by taking the offset) Thanks, Janosch Am 03.03.2015 um 08:32 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: I don't know, esp since it is an approximation to begin with. An alternative is to take the offsets from your multi-time-point subjects and the single maps from your subjects with one time point and run that through the one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then you should subtract the mean age of the one time-point subjects from the age of the multi-time point subjects before the 1st stage of analysis. doug On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote: Hi Doug, thank you very much for your answer! Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: You would do the long analysis using a random effects analysis. OK, so basically do 2-stage modeling (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right? For each subject you can get a slope (this won't work if the subject only has 1 time point), then concatenate the slopes into a file and run mri_glmfit, then follow the procedures from the archive email you reference. One quarter of my subjects only has one measurement time point. Can I still use this method (which would only consider the 3/4 of the subjects) to correct clusters found in the whole group? Or would it only be valid for correcting clusters from an LME model for the reduced group? Thanks, Janosch doug On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote: Hi Doug and others, I would like apply (Monte Carlo simulation) cluster correction (as opposed to the implemented vertex-wise FDR correction) on the results from a longitudinal study I analyzed using the LME toolbox. The design is unbalanced (different number of time points, from 1 to 4, per subject). In this thread (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) you, Doug, suggested, if I understand correctly: - concatenating the images using `mris_preproc --paired-diff` - smooth with the same kernel size as used in the lme analysis - running `mri_glmfit` on them with an fsgd file that uses the same covariates and the same contrast (excluding the interaction term with time) as used in the lme analysis - overwriting sig.mgh with the one from the lme analysis - running `mri_glmfit-sim --cache` How would I extend this to my case where I don't have pairwise images, but 1 image for some participants, for others up to 4? Thanks a lot, Janosch -- 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/ 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/ -- 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
Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface
It looks like you made your txt file under windows which creates an obscure situation where there are carriage returns instead of line feeds and that causes the error. If you run 'more my_parcstats.txt' you see a bunch of ^M strings. So, you'll need to recreate it under a linux system. doug On 03/03/2015 05:50 PM, Jin, Tony wrote: Hi Dr. Greve (and co.), Good to hear that I’m using a proper command, but alas, visualizing the surface overlay file using tksurfer confirmed that my stats didn’t transfer. I believe I’m calling tksurfer correctly, since I replaced the lh.parcstats file with lh.thickness, and a cortical thickness heat map overlaid just fine. Would you please confirm that my parcstats.txt file is arranged correctly? It is an ascii file with 36 lines. Here are the first few: ctx-lh-bankssts 0.905 ctx-lh-caudalanteriorcingulate 0.838 ctx-lh-caudalmiddlefrontal 0.922 ctx-lh-cuneus 0.892 And here are my calls: To generate overlay file: mris_convert --annot lh.aparc.annot --parcstats parcstats.txt lh.pial *lh.parcstats* — new desired annotation file To visualize overlay file mapped onto lh.pial surface using Tksurfer: tksurfer subject lh pial -overlay *lh.parcstats* To convert overlay file to ASCII for validation: mris_convert -c *lh.parcstats* lh.pial lh.parcstats.asc I tried doing this with version 5.3.0 on both Mac and Linux platforms and got the same results (zeroes across all vertices). If it helps, I’ve attached both my —parcstats text file and the resulting overlay file. Any ideas as to how I can successfully transfer my stats onto a surface overlay file? Thank you for your assistance, Tony Tony Jin Data Technician Dept. of Psychiatry Stony Brook Medicine From: Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Reply-To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, March 3, 2015 at 11:43 AM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface That is the right way (or one of them). Did you look at the result in tksurfer? On 03/03/2015 11:34 AM, Jin, Tony wrote: Hi all, I’d like to map my own stats (one value per Desikan-Killiany region) onto a subject's surface file, to create a figure similar to the following: http://openi.nlm.nih.gov/detailedresult.php?img=3280212_pone.0031913.g001req=4 To do this, I tried to create a scalar overlay file using mris_convert’s --parcstats option, per the following mris_convert example: “” Create a scalar overlay file where each parcellation region contains a single value: mris_convert \ --annot lh.aparc.annot \ --parcstats lh.parcstats.txt \ lh.white \ lh.parcstats (...) --parcstats infile is the name of text file containing label/val pairs, where label is an annot name and val is a value associated with that label. “” However, looking at the output file, stats didn’t seem to map to any vertices; instead, I observed zeroes across all in both Freeview and after conversion to ASCII (see first few lines below). I tried a few other ways to delimit the “label/val” pairs of the --parcstats file, including using tab, space, and forward-slash, but each way seemed to produce the same results: 000 -10.67346 -71.19921 6.09064 0.0 001 -11.29567 -71.20504 6.32133 0.0 002 -12.26970 -71.62605 6.00416 0.0 003 -13.11823 -71.40913 6.45834 0.0 004 -14.22002 -71.39742 6.28750 0.0 So, I wonder: is using mris_convert with the --parcstats flag a correct way to create such a map? If so, what could have gone wrong? If not, what’s the easiest way to map my own regional stats onto a surface? Your expertise is greatly appreciated; Thanks and all the best, Tony Jin Data Technician Dept. of Psychiatry Stony Brook Medicine This e-mail message, including any attachments, 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 e-mail and destroy all copies of the original. ___ 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:
Re: [Freesurfer] tksurfer overlay threshold
I'm not sure what you mean. optimal in what sense? doug On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: Hi Fs experts, I had a quick question about settings thresholds of surface overlays in Tksurfer. I am currently generating images of the thickness, volume and surface area of individual subjects, and would like to know if there are optimal minimum and maximum threshold values to be set for different surfaces. For example, when overlaying thickness (from /surf/?h.thickness), I have set the min threshold to 1 or 1.3 (see attached); however I'm not sure this same threshold holds up in the other surfaces (e.g. surface area). In summary, is there an optimal way to determine what this min. and max. threshold should be in function of the distribution displayed in the threshold window (see attached, on the left)? Thank you! Gabriella ___ 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] tksurfer overlay threshold
you can use the command: set_current_threshold_from_percentile(min, mid,max) which will compute the thresholds based on the histogram of values On Tue, 3 Mar 2015, Douglas N Greve wrote: I'm not sure what you mean. optimal in what sense? doug On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: Hi Fs experts, I had a quick question about settings thresholds of surface overlays in Tksurfer. I am currently generating images of the thickness, volume and surface area of individual subjects, and would like to know if there are optimal minimum and maximum threshold values to be set for different surfaces. For example, when overlaying thickness (from /surf/?h.thickness), I have set the min threshold to 1 or 1.3 (see attached); however I'm not sure this same threshold holds up in the other surfaces (e.g. surface area). In summary, is there an optimal way to determine what this min. and max. threshold should be in function of the distribution displayed in the threshold window (see attached, on the left)? Thank you! Gabriella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] from vol timecourse to surf timecourse
You can use something like rawfunc2surf-sess -i fstcmc -hemi lh -fwhm 5 -o fstcmc.sm05.fsaverage.lh.nii.gz Then in mkanalysis-sess, use -funcstem fstcmc.sm05.fsaverage.lh (and do not include preprocessing options) doug On 03/03/2015 02:12 PM, Jan Willem Koten wrote: Dear Surfer experts, (Most likely Dough) It is common practice to perform the slice time correction first and than the motion correction. However free surfer seems to work in the opposite way. I have tried to write a mini matlab freesurfer script for the common way. system(['stc-sess -s 'funcdir(i).name ' -i f -o fstc -so siemens']) system(['mc-sess -s 'funcdir(i).name ' -fstem fstc -fmcstem fstcmc -per-run']) This seems to work. My problem is how do I get the resulting fstcmc.ni.gz on to the fsaverage surface using spherical alignment? Jan ___ 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] Mapping Own DK Regional Stats onto Surface
Hi Doug and co., To follow up about this: I may have resolved the issue. For posterity, label names of the mris_convert --parcstats file should be created without the ctx-?h” prefix: My parcstats file previously read... ctx-lh-bankssts 0.905 ctx-lh-caudalanteriorcingulate 0.838 ctx-lh-caudalmiddlefrontal 0.922 ctx-lh-cuneus 0.892 ... But should have read... bankssts 0.905 caudalanteriorcingulate 0.838 caudalmiddlefrontal 0.922 cuneus 0.892 ... Here’s an example of a successful output message: reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) label: bankssts, val: 0.90471 label: caudalanteriorcingulate, val: 0.83800 label: caudalmiddlefrontal, val: 0.92191 label: cuneus, val: 0.89220 label: entorhinal, val: 0.59121 label: frontalpole, val: 0.74679 label: fusiform, val: 0.93415 label: inferiorparietal, val: 0.92599 label: inferiortemporal, val: 0.95396 label: insula, val: 0.87674 label: isthmuscingulate, val: 0.88986 label: lateraloccipital, val: 0.93415 label: lateralorbitofrontal, val: 0.91696 label: lingual, val: 0.90705 label: medialorbitofrontal, val: 0.85372 label: middletemporal, val: 0.95222 label: paracentral, val: 0.91375 label: parahippocampal, val: 0.77710 label: parsopercularis, val: 0.93823 label: parsorbitalis, val: 0.92425 label: parstriangularis, val: 0.94988 label: pericalcarine, val: 0.84703 label: postcentral, val: 0.93590 label: posteriorcingulate, val: 0.93998 label: precentral, val: 0.96708 label: precuneus, val: 0.95396 label: rostralanteriorcingulate, val: 0.92278 label: rostralmiddlefrontal, val: 0.95222 label: superiorfrontal, val: 0.95979 label: superiorparietal, val: 0.95075 label: superiortemporal, val: 0.93094 label: supramarginal, val: 0.95222 label: temporalpole, val: 0.27797 label: transversetemporal, val: 0.90879 Many thanks for your responsiveness; have a great night! Tony Jin Data Technician Dept. of Psychiatry Stony Brook Medicine From: Jin, Tony Jin tony@stonybrookmedicine.edumailto:tony@stonybrookmedicine.edu Reply-To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, March 3, 2015 at 6:28 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface Thank you for discovering this text file issue. I’ve corrected its formatting, reran the command, but unfortunately the overlay file issue persists. The following is the Terminal I/O; once again, I’ve also attached the parcstats file and the output overlay file for reference. mris_convert --annot /sub1/label/lh.aparc.annot --parcstats /20150302_map_and_edits/parcstats_properly_formatted.txt /sub1/surf/lh.pial /20150302_map_and_edits/lh.parcstats.overlay reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Any thoughts or suggestions would be greatly appreciated; Tony From: Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu Reply-To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Tuesday, March 3, 2015 at 5:59 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mapping Own DK Regional Stats onto Surface It looks like you made your txt file under windows which creates an obscure situation where there are carriage returns instead of line feeds and that causes the error. If you run 'more my_parcstats.txt' you see a bunch of ^M strings. So, you'll need to recreate it under a linux system. doug On 03/03/2015 05:50 PM, Jin, Tony wrote: Hi Dr. Greve (and co.), Good to hear that I’m using a proper command, but alas, visualizing the surface overlay file using tksurfer confirmed that my stats didn’t transfer. I believe I’m calling tksurfer correctly, since I replaced the lh.parcstats file with lh.thickness, and a cortical thickness heat map overlaid just fine. Would you please confirm that my parcstats.txt file is arranged correctly? It is an ascii file with 36 lines. Here are the first few: ctx-lh-bankssts 0.905 ctx-lh-caudalanteriorcingulate 0.838 ctx-lh-caudalmiddlefrontal 0.922 ctx-lh-cuneus 0.892 And here are my calls: To generate overlay file: mris_convert --annot lh.aparc.annot --parcstats parcstats.txt lh.pial *lh.parcstats* — new desired annotation file To visualize overlay file
Re: [Freesurfer] Monte Carlo simulation - Longitudinal Pipeline
Hey Doug, thanks again! That means, I would do something like: 1.) construct longitudinal qdec table - only use fsid, fsid-base, and years/age columns - substract the average age of the one-time point subjects from years/age value for every subject at every time point 2.) run long_mris_slopes - use the --do-avg flag? 3.) concatenate the output files from 2) and the maps from the one-time point subjects with mris_preproc - use --is flag to select maps by specifying full path 4.) run mri_glmfit - use --osgm flag for one-sample group mean 5.) replace sig.mgz file with the one from LME analysis and run mri_glmfit-sim Is that correct? (especially, is using --do-avg what you meant by taking the offset) Thanks, Janosch Am 03.03.2015 um 08:32 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: I don't know, esp since it is an approximation to begin with. An alternative is to take the offsets from your multi-time-point subjects and the single maps from your subjects with one time point and run that through the one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then you should subtract the mean age of the one time-point subjects from the age of the multi-time point subjects before the 1st stage of analysis. doug On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote: Hi Doug, thank you very much for your answer! Am 02.03.2015 um 11:30 schrieb Douglas N Greve gr...@nmr.mgh.harvard.edu: You would do the long analysis using a random effects analysis. OK, so basically do 2-stage modeling (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right? For each subject you can get a slope (this won't work if the subject only has 1 time point), then concatenate the slopes into a file and run mri_glmfit, then follow the procedures from the archive email you reference. One quarter of my subjects only has one measurement time point. Can I still use this method (which would only consider the 3/4 of the subjects) to correct clusters found in the whole group? Or would it only be valid for correcting clusters from an LME model for the reduced group? Thanks, Janosch doug On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote: Hi Doug and others, I would like apply (Monte Carlo simulation) cluster correction (as opposed to the implemented vertex-wise FDR correction) on the results from a longitudinal study I analyzed using the LME toolbox. The design is unbalanced (different number of time points, from 1 to 4, per subject). In this thread (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) you, Doug, suggested, if I understand correctly: - concatenating the images using `mris_preproc --paired-diff` - smooth with the same kernel size as used in the lme analysis - running `mri_glmfit` on them with an fsgd file that uses the same covariates and the same contrast (excluding the interaction term with time) as used in the lme analysis - overwriting sig.mgh with the one from the lme analysis - running `mri_glmfit-sim --cache` How would I extend this to my case where I don't have pairwise images, but 1 image for some participants, for others up to 4? Thanks a lot, Janosch -- 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/ 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] -addtp option not working in recon-all -long
Thanks Martin. It works now.
On Mon, Mar 2, 2015 at 10:51 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu
wrote:
Hi Bishesh,
it is a know bug. in your recon-all find this block (should be in line
6148)
if ( ! $found_tpNid ) then
echo ERROR: $tpNid is not in
${longbasedir}/${BaseSubjsListFname}
echo
exit 1
endif
and replace the first line (if statement) with:
if ( ! $found_tpNid ! $DoAddTp ) then
Best, Martin
On 02/25/2015 05:21 PM, Bishesh Khanal wrote:
It's 5.3.0. Here is the freesurfer version and my system info:
Build stamp: freesurfer-Linux-centos6_x86_
64-stable-pub-v5.3.0
RedHat release: Fedora release 19 (Schrödinger’s Cat)
Kernel info: Linux 3.14.22-100.fc19.x86_64 x86_64
On Wed, Feb 25, 2015 at 7:54 PM, Martin Reuter
mreu...@nmr.mgh.harvard.edu wrote:
Hi Bishesh,
that is weird, it should add the time point to that file. What version of
FS are you using?
Best, Martin
On 02/25/2015 06:03 AM, Bishesh Khanal wrote:
Hi all,
I wanted to add a new timepoint in my longitudinal stream without
recreating the base template. recon-all -help shows that I should be able
to do that with:
recon-all -long tpNsubjid longbasesubjid -addtp -all
However, when I tried it I get an error.
Here is the error:
$recon-all -long miriad_189_AD_M_10SimulatedT1From01
miriad_189_AD_M_01_10 -addtp -all
ERROR: miriad_189_AD_M_10SimulatedT1From01 is not in
/home/bkhanal/works/freesurfer/freesurferSubjects/miriad_189_AD_M_01_10/base-tps
Since I'm using a new timepoint which was not used in creating the base
template it would of course not be in base-tps. Is -addtp no having any
effect here ?
The freesurfer version and my system info:
Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
RedHat release: Fedora release 19 (Schrödinger’s Cat)
Kernel info: Linux 3.14.22-100.fc19.x86_64 x86_64
Thanks,
Bishesh
___
Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Dr. Martin Reuter
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.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.
___
Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Dr. Martin Reuter
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129
Phone: +1-617-724-5652
Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
Web : http://reuter.mit.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.
___
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
Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Doug,
Thanks I had hoped to use mri_mask but was foiled in my attempt to convert the
.label files to .mgz using mri_label2bvol. I assumed I must be on the wrong
track.
my command was
mri_label2vol --label V2_lh.label --temp f.nii.gz --reg register.dat
--fillthresh .3 --proj frac 0 1 .1 --subject V2_subject5 --hemi lh --o V2_lh.mgz
I have previously used this command successfully to convert labels for usage in
FSL. The volume will display using tkmedit on the orig surface, but in tksurfer
using the inflated surface there is nothing visible when attempting to open as
an overlay.
I have played around with different options and attempted to move forward to
mri_mask using the V2_lh.mgz file (hoping to later open the data in tksurfer)
but the command
mri_mask -transfer 255 -keep_mask_deletion_edits masked_data V2_lh.mgz
lh_colour.mgz V2_colour_lh.mgz
gives
transfer mask voxels=255 to dst vol
Transferring mask edits ('1' voxels) to dst vol
ERROR: dimension mismatch between source and mask
I assume I must be missing something fundamental in the mri_label2vol command?
Thank you for your help
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sarah Finnegan
[sarah.finne...@stcatz.ox.ac.uk]
Sent: 26 February 2015 15:12
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Bruce
Thanks for your reply,
I did use mri_vol2surf for the sampling
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {out file name} --out_type {mgz}
I don't believe that I want to average within the ROI. I want to take any
clusters of activity within V2 and feed this into a script i'm developing in
MATLAB to work out the distance between different voxel clusters and the size
of each cluster, but only for within my region defined as V2. Hopefully that
makes sense, If I average I think I will lose this spatial information?
Thanks
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 26 February 2015 15:04
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Sarah
have you used mri_vol2surf to sample the data onto the surface? When you
say extract specific regions of functional data from a flat do you
want to average within the ROI?
cheers
Bruce
On Thu, 26 Feb 2015, Sarah Finnegan wrote:
I have a question about the equivalent of fslmaths -mas option in
freesurfer.
I have several manually defined labels in .label form that I want to use to
extract specific regions of functional data from a flat patch. Ordinarily in
fsl I would just use
fslmaths -invol {functional_data} -mas {bin_label} -outvol
{masked_functional_data}
but I'm a little confused about an equivalent for this in free surfer as I
don't want to perform any further stats on these ROI yet, extract them from
any surrounding data and overlay onto the flattened surface.
I have tried using
mri_vol2roi --label {V2_rh.label} --srcvol {functional_data.mgz} --srcreg
{anat2exf.register.dat} --roiavg {func_V2_mask} --finalmskvol
{func_V2_mask_out}
but when overlaying the output file there are no data points visible.
Any help would be great as several other functions that I have tried seem to
be obsolete,
Thanks!
Sarah
___
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] equivalent for fslmaths -mas option in freesurfer
On 3/3/15 9:41 AM, Sarah Finnegan wrote:
Hi Doug,
Thanks I had hoped to use mri_mask but was foiled in my attempt to convert
the .label files to .mgz using mri_label2bvol. I assumed I must be on the
wrong track.
my command was
mri_label2vol --label V2_lh.label --temp f.nii.gz --reg register.dat
--fillthresh .3 --proj frac 0 1 .1 --subject V2_subject5 --hemi lh --o
V2_lh.mgz
I have previously used this command successfully to convert labels for usage
in FSL. The volume will display using tkmedit on the orig surface, but in
tksurfer using the inflated surface there is nothing visible when attempting
to open as an overlay.
I'm not sure what you mean here by it displays in tkmedit on the orig
surface. Can you elaborate? What was your tksurfer command. Also, try a
fillthresh of 0 as there may be few voxels that have more than 30%.
I have played around with different options and attempted to move forward to
mri_mask using the V2_lh.mgz file (hoping to later open the data in tksurfer)
but the command
mri_mask -transfer 255 -keep_mask_deletion_edits masked_data V2_lh.mgz
lh_colour.mgz V2_colour_lh.mgz
gives
transfer mask voxels=255 to dst vol
Transferring mask edits ('1' voxels) to dst vol
ERROR: dimension mismatch between source and mask
I assume I must be missing something fundamental in the mri_label2vol command?
Not sure what you are trying to do in that command. Where did
lh_colour.mgz come from?
doug
Thank you for your help
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Sarah Finnegan
[sarah.finne...@stcatz.ox.ac.uk]
Sent: 26 February 2015 15:12
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Bruce
Thanks for your reply,
I did use mri_vol2surf for the sampling
mri_vol2surf --src {zstat1} --srcreg {anat2exf.register.dat} --hemi
{hemi}--projfrac {0.8} --out {out file name} --out_type {mgz}
I don't believe that I want to average within the ROI. I want to take any
clusters of activity within V2 and feed this into a script i'm developing in
MATLAB to work out the distance between different voxel clusters and the size
of each cluster, but only for within my region defined as V2. Hopefully that
makes sense, If I average I think I will lose this spatial information?
Thanks
Sarah
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: 26 February 2015 15:04
To: Freesurfer support list
Subject: Re: [Freesurfer] equivalent for fslmaths -mas option in freesurfer
Hi Sarah
have you used mri_vol2surf to sample the data onto the surface? When you
say extract specific regions of functional data from a flat do you
want to average within the ROI?
cheers
Bruce
On Thu, 26 Feb 2015, Sarah Finnegan wrote:
I have a question about the equivalent of fslmaths -mas option in
freesurfer.
I have several manually defined labels in .label form that I want to use to
extract specific regions of functional data from a flat patch. Ordinarily in
fsl I would just use
fslmaths -invol {functional_data} -mas {bin_label} -outvol
{masked_functional_data}
but I'm a little confused about an equivalent for this in free surfer as I
don't want to perform any further stats on these ROI yet, extract them from
any surrounding data and overlay onto the flattened surface.
I have tried using
mri_vol2roi --label {V2_rh.label} --srcvol {functional_data.mgz} --srcreg
{anat2exf.register.dat} --roiavg {func_V2_mask} --finalmskvol
{func_V2_mask_out}
but when overlaying the output file there are no data points visible.
Any help would be great as several other functions that I have tried seem to
be obsolete,
Thanks!
Sarah
___
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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
