Re: [Freesurfer] FW: Monte Carlo Simulation
can you upload your glmdir to our filedrop (see end of email) doug On 03/10/2015 02:13 PM, Wolthusen, Rick Peter Fritz wrote: Hi FS Community, I emailed with Doug a week ago with regards to limiting the results of a PASL Regression analysis to subcortical areas only in the tal output file (see below). I redid the analysis from scratch adding the flag --mask $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to the above mentioned mask with regards to the used Mask Vol.. However, the only peak I get after the MCS is still in the cortical area. I am more interested in the subcortical regions though - what else can I do to limit the results to the subcortical regions of interest only? Thanks, Rick From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, March 02, 2015 4:10 PM To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu Subject: Re: Monte Carlo Simulation Hi Rick, in the future please post to the list and not to us personally. Thanks! When you did the volume-based analysis, it should have masked out anything anything that was not subcortical. Did it not? If not, then when you run mri_glmfit you can add --mask $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick. doug On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug, I was running the following command in launchpad in order to correct for multiple comparison (using a output file from a PASL FS analysis): pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0 cbf.talairach_p01_abs_montecarlo When I looked for the surviving clusters, I just found clusters in the cortical area but not in sub-cortical areas (the cortical clusters where consistent with the clusters I found in the cortical analyses though). Is there a way I can limit the Monte Carlo Simulation to sub-cortical areas only so that I'll also see the most sgn. clusters in the sub-cortical areas? Please let me know if you have any additional questions! Thanks, Rick -- 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] segmentation of the thalamus?
Dear FreeSurfer developers and users, I’m wondering if any of you worked on further segmentation of the thalamus into thalamic nuclei or e.g. dorsal vs. medial thalamus. Thanks, Bengi Bengi Baran, Ph.D. Post-Doctoral Fellow Martinos Center for Biomedical Imaging Harvard Medical School Massachusetts General Hospital 149 13th Street Charlestown Navy Yard Charlestown, MA 02129 email: bba...@partners.orgmailto:bba...@partners.org phone: 617-643-7964 fax: 617-726-4078 https://sleep.med.harvard.edu/people/trainees/1598/Bengi+Baran+MA+PhD ___ 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] Monte Carlo Simulation
Sorry, I don't have time to deconstruct that script. Can you simplify it for me? On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote: This is the script I am using to create cbf.talaraich.mgz (attached). Thanks, Rick 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: Wednesday, March 11, 2015 3:22 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Something went very wrong with your first level analysis because the final mask is pretty messed up. how did you create cbf.talairach.mgz ? On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug et al., Here is the glmdir file you were requesting: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928 Thanks, Rick From: Wolthusen, Rick Peter Fritz Sent: Tuesday, March 10, 2015 2:10 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: RE: Monte Carlo Simulation Hi FS Community, I emailed with Doug a week ago with regards to limiting the results of a PASL Regression analysis to subcortical areas only in the tal output file (see below). I redid the analysis from scratch adding the flag --mask $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to the above mentioned mask with regards to the used Mask Vol.. However, the only peak I get after the MCS is still in the cortical area. I am more interested in the subcortical regions though - what else can I do to limit the results to the subcortical regions of interest only? Thanks, Rick From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, March 02, 2015 4:10 PM To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu Subject: Re: Monte Carlo Simulation Hi Rick, in the future please post to the list and not to us personally. Thanks! When you did the volume-based analysis, it should have masked out anything anything that was not subcortical. Did it not? If not, then when you run mri_glmfit you can add --mask $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick. doug On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug, I was running the following command in launchpad in order to correct for multiple comparison (using a output file from a PASL FS analysis): pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0 cbf.talairach_p01_abs_montecarlo When I looked for the surviving clusters, I just found clusters in the cortical area but not in sub-cortical areas (the cortical clusters where consistent with the clusters I found in the cortical analyses though). Is there a way I can limit the Monte Carlo Simulation to sub-cortical areas only so that I'll also see the most sgn. clusters in the sub-cortical areas? Please let me know if you have any additional questions! Thanks, Rick -- 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 -- 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 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
[Freesurfer] FW: Monte Carlo Simulation
Hi FS Community, I emailed with Doug a week ago with regards to limiting the results of a PASL Regression analysis to subcortical areas only in the tal output file (see below). I redid the analysis from scratch adding the flag --mask $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to the above mentioned mask with regards to the used Mask Vol.. However, the only peak I get after the MCS is still in the cortical area. I am more interested in the subcortical regions though - what else can I do to limit the results to the subcortical regions of interest only? Thanks, Rick From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, March 02, 2015 4:10 PM To: Wolthusen, Rick Peter Fritz; Freesurfer@nmr.mgh.harvard.edu Subject: Re: Monte Carlo Simulation Hi Rick, in the future please post to the list and not to us personally. Thanks! When you did the volume-based analysis, it should have masked out anything anything that was not subcortical. Did it not? If not, then when you run mri_glmfit you can add --mask $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and that should do the trick. doug On 02/25/2015 03:22 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug, I was running the following command in launchpad in order to correct for multiple comparison (using a output file from a PASL FS analysis): pbsubmit -m riwohoy -q extended -c mri_glmfit-sim --glmdir tal.sm.PDI21.con.12and32ch.n74.glm --sim-sign abs --sim mc-z 1 2.0 cbf.talairach_p01_abs_montecarlo When I looked for the surviving clusters, I just found clusters in the cortical area but not in sub-cortical areas (the cortical clusters where consistent with the clusters I found in the cortical analyses though). Is there a way I can limit the Monte Carlo Simulation to sub-cortical areas only so that I'll also see the most sgn. clusters in the sub-cortical areas? Please let me know if you have any additional questions! Thanks, Rick -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem with Longitudinal QDEC file and mris_preproc
Hi Martin, Thank you for your help and clarifications. I did run the *_to_table commands and now my LME analyses are running smoothly. Best, Jennifer Legault On Mon, Mar 9, 2015 at 11:35 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Jennifer, if you are interested in volumes from the stats file, you need to use aseg_stats_to_table and aparc_stats… to stack those data across subjects and time points into a single table that you then analyze with the LME tools. mris_preproc is only for stacking surface maps. The longitudinal QDEC file can be the same, you only need it to tell aseg_stats_2_table etc how to create the file names for the individual *.long.* directories. So that file only needs 2 columns (fsid, fsid-base ) for that. And maybe you want to pass other covariates (e.g. time from baseline, average age, gender etc) into LME via that same qdec table. The FS stats (e.g. either thickness maps, or stats tables) will be read separately. If you still have difficulties with the long QDEC file, try using space separated instead of tab! You don’t smooth the volume data. Look at the *_to_table commands to generate the tables. Best, Martin On Mar 6, 2015, at 5:09 PM, Jennifer Legault jlegaul...@gmail.com wrote: Hi all, I am new to Freesurfer and have run my participants’ data through the longitudinal preprocessing stream and am now trying to assemble my data so that they can be put into a linear mixed effect model analysis. While the longitudinal tutorial with cortical thickness data is very helpful, I am interested in GM volume (specific ROIs in aseg. + the lh and rh aparc. files) and have run into a few problems. 1) Problem with mris_preproc command/with QDEC file: a) I have made a Longitudinal QDEC file (attached in this comment as an excel file and .dat file) and I made sure to export to my Subjects dir, and then put in the following command: mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh --meas volume --out lh.volume.mgh When I run this command, it only runs for my first participant (which it takes from the Longitudinal QDEC file, such that if I take out the first row of the QDEC file, it starts with the next participant) I do not receive any sort of error message or anything, it just doesn’t keep running. Furthermore, I cannot find the output file (lh.volume.mgh) anywhere in my subjects directory. b) I am also wondering whether I need to make separate QDEC files for 1) aseg data 2) lh.aparc and 3) rh.aparc. Right now, my QDEC file has all of the information of interest in one place. c) I made the QDEC file in excel, and saved it as tab delimited (when I try to save it as space delimited (.prn--which I rename as .dat) and re-open it, it loses many of my headers and data). Does it have to be space delimited, and if so, is there another way of formatting it as space delimited? If not, then is there something else wrong with my QDEC format? 2) I do not know whether I am supposed to smooth the volume stack. According to my understanding of the Longitudinal tutorial, we should first run mris_preproc to concatenate our files and resample volume data to a common subject. Next, we should smooth the stacked/concatenated file. Should I use the following command: mri_vol2surf --src input file --hemi hemisphere --fwhm 10 --out outpufile Thank you for taking the time to read this email, I sincerely appreciate it. Best, Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University long.qdec.table.xlsxlong.qdec.table.dat___ 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. -- Jennifer Legault Ph.D candidate, Neuroscience Brain, Language, and Computation Lab The Pennsylvania State University ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] aparc superior occipital lobe labeled as superior parietal
From Rahul Desikan: -- Forwarded message -- From: Rahul Desikan rahuldesi...@gmail.com To: paulo.ba...@usp.br, freesurfer@nmr.mgh.harvard.edu Cc: Date: Wed, 11 Mar 2015 08:42:31 -0700 Subject: Re: [Freesurfer] aparc superior occipital lobe labeled as superior parietal (fwd) Hi Paulo, This is a good question/observation. From a neuroradiology perspective, we often struggle with the lateral boundary between the occpital and parietal cortices, often referring to these areas as 'parieto-occipital region'. The medial boundary is a lot easier given the parieto-occipital incisure (sulcus). Nevertheless, I think it would be worthwhile to revisit this region (along with others in my parcellation atlas) to see if we can come up with a more robust delineation. For example, I suspect we may be able to carry forth the parieto-occipital incisure into the lateral hemisphere thus serving as a guide to differentiate between the two cortices laterally. For your immediate purposes, I suspect the aparc2009 atlas would be better for evaluating the posterolateral occipital and parietal cortices. Warm regards, Rahul On Wed, 11 Mar 2015, paulo.ba...@usp.br wrote: Hi everybody I was looking at my subjects and I noted that the superior occipital region is labeled as superior parietal cortex in the aparc parcelation. Then I discovered that the bert subject, that comes as reference with freesurfer, and that the fsaverage also have their superior occipital cortex labeled as superior parietal cortex. I just asked the freesurfer instructors at an organized freesurfer course and was intructed to post this observation to the list. I guess this happens because there is no superior occipital label in the aparc partcelation. The aparc2009 has it, and the occipital and parietal cortices are labeled correctly. Has anyone noticed this before? I guess that if the parietal and/or occipital lobe are the regions of interest of the study, the aparc2009 parcelation should be used. Best regards Paulo Bazán ___ 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] newbie questions: transform RAS vectors to talaraich vectors and view
Dear List, I have sets of vectors in RAS coordinates from many volunteers. I want to transform them into coordinates for a standard volume. (1) I presume the standard volume that makes sense to use is orig.mgz in $FREESURFER_HOME/subjects/fsaverage/mri. Please confirm. (2)I presume that I can transform the vectors contained in subject N's .label files to talairaich coordinates using the transform in $FREESURFER_HOME/subjects/subjectN/mri/transforms/talairach.xfm. Please confirm. (3)What tool can I use to convert orig.mgz into a sequence of axial cuts in some standard graphics format, e.g. gif, png, tiff? Thanks and best regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh ___ 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] Annualised percentage change within linear mixed models
Hi FreeSurfer team, I was wondering if it is possible to use a measure of annualised percentage change instead of raw thickness within the FreeSurfer toolbox for Matlab (i.e. when running linear mixed models)? Thanks for your help, Nandi ___ 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] GLM analysis on CBF maps
For the intercept, you are testing for a difference in the mean CBF
between the groups regressing out the effects of gender and age.
For the slope, you are testing for an interaction between group and age
regressing out the effects of gender.
doug
On 3/12/15 1:30 PM, Matthieu Vanhoutte wrote:
Hello,
I have run GLM group analyses with Freesurfer tools according DODS
model, with six classes ((Male,Female) ; (Control,Left,Right)) and one
age variable :
/Class MaleControl
Class MaleLeft
Class MaleRight
Class FemaleControl
Class FemaleLeft
Class FemaleRight
Variables Age /
I wanted to test /Control Left/ and /Control Right/ on CBF maps. I
defined with help of the tutorial contrats for that :
/control-left.intercept.mtx : 0.5 -0.5 0 0.5 -0.5 0 0 0 0 0 0 0
control-left.slope.mtx : 0 0 0 0 0 0 0.5 -0.5 0 0.5 -0.5 0
control-right.intercept.mtx : 0.5 0 -0.5 0.5 0 -0.5 0 0 0 0 0 0
control-right.slope.mtx : 0 0 0 0 0 0 0.5 0 -0.5 0.5 0 -0.5/
My problem is that I don't know how to interpret significative results
in both /Control Left /contrasts/: //control-left.intercept.mtx
/and///control-left.slope.mtx. /The same for/Control Right./ One is
coding for intercept and the other for slope, but concretely what
significative results in both contrasts mean ?
Thank you in advance for helping !
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2015-03-11 16:51 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu:
the sig value is actually -log10(p)*sign(gamma) where gamma
is the
contrast (gamma.mgh). The p-value is two-tailed, and the color
indicates
what tail you are on.
doug
On 03/10/2015 01:21 PM, Matthieu Vanhoutte wrote:
Dear FreeSurfer's experts,
I have launched a GLM analyses following the tutorial :
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Below the command I have used :
/mri_glmfit \
--y
${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.all.subjects.fwhm3.fsaverage.cbf_s.mgh
\
--fsgd ${FS_DIR}/SurfaceAnalysis_mri_glmfit/g6v1.fsgd dods \
--C
${FS_DIR}/SurfaceAnalysis_mri_glmfit/control-left.intercept.mtx \
--surf fsaverage lh \
--cortex \
--glmdir ${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/
In order to see the uncorrected results with p.0001, I ran :
/freeview -f
${SUBJECTS_DIR}/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=${SUBJECTS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/control-left.intercept/sig.mgh:overlay_threshold=4,5
-viewport 3d/
However, nothing appears with this threshold and when I wanted to
configure overlay I saw that most of my values in /sig.mgh /were
negatives between -4 and 0...
How is possible for /-log10(pvalue)/ values ? Could I obtain
significant uncorrected values from this /sig.mgh/ file ?
Please find attached my needed files : *y.fsgd, mri_glmfit.log,
**/control-left.intercept.mtx/ and sig.mgh *
Thank you in advance for helping me !!
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358
Fax: 617-726-7422 tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
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Compliance HelpLine at
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but does not contain patient information, please contact the
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dispose of the e-mail.
Re: [Freesurfer] Monte Carlo Simulation
Yes, that probably is the reason. doug On 3/12/15 4:31 PM, Wolthusen, Rick Peter Fritz wrote: To be honest, I checked the between subject alignment and it looked pretty good. None of my subjects was way out of alignment. However, since we cannot fit the whole brain in the slice during scanning, we are always cutting of the top of the brain, sometimes more, sometimes less, depending on the brain size. Could this be the reason why the mask is off? If not, is there anything else I can check? 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: Thursday, March 12, 2015 2:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I meant which ones are causing the problems when you run mri_glmfit. When you run fslview you will see something that looks like a brain. As you scroll thru the different time points, you'll see the CBF maps for different subjects. They should be more-or-less in alignment. Look for ones that are way out of alignment or don't have all of the brain. On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote: Well, I checked the proper match of ASL and anatomical scans again and one of the subjects I reported before was indeed wrongly matched. Thanks! What do you mean with So the next thing I would do is to find which subjects are the ones that are off.? You mean off when I check for registration? That's what I did before with tkregister2 and they all looked fine to me. What do I look for when I open the cbf.talaraich.nii.gz file in fslview? 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: Thursday, March 12, 2015 12:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation If the registration looks ok, then that is all that counts. However, I'm a bit sceptical that the reg looks ok but the mincost is that much different than the others. You should double check that the ASL is properly matched with the corresponding anatomical (ie, it is not two different subjects). This would also not explain why the masks were so far off. So the next thing I would do is to find which subjects are the ones that are off. You can do this with something like fslview y.nii.gz where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit (you can mri_convert it to nii.gz). You can then step through each frame (or play them as a movie) to see if any look odd. The mincost is from the BBR cost function. It is basically the mean gray/white contrast across cortex passed through a sigmoid function to make its range 0-1, 0 being best. You cannot necessarily generalize the normal range for one modality to that of another. On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug et al., I indeed found 3 subjects, whose registration looked ok when I eyeballed them with the tkregister 2 command, with values of .9 and higher (all the other subjects had values between .44 and .61). Do you recommend to redo the analysis without them or to run the first level analysis again with --init-spm instead of --init-fsl in bbregister? Also, how is the first value in the .mincost file generated and what does it mean? Can you use this file for other modalities, too? Let's say if I want to do the first level analysis for fct. connectivity instead of PASL for example? Thanks, Rick 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: Wednesday, March 11, 2015 6:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation For the range, lower is better, but it impossible to say exactly what is good enough because it depends on your data. If it is 0.8 or higher, then that is probably bad. What I'm hoping is that there will be one or two outliers. The --init-spm was in place of --init-fsl in bbregister. But you only need that if you find a bad registration. On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote: I checked registration before and it was fine. However, I'll go back and look at the first value in the aslcal.reg.mincost file. What is the normal range? Also, I don't understand what you mean with the FSL initialization fails and try --init-spm - can you please give me some more information? Thanks! 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: Wednesday, March 11, 2015 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte
Re: [Freesurfer] Monte Carlo Simulation
If the registration looks ok, then that is all that counts. However, I'm a bit sceptical that the reg looks ok but the mincost is that much different than the others. You should double check that the ASL is properly matched with the corresponding anatomical (ie, it is not two different subjects). This would also not explain why the masks were so far off. So the next thing I would do is to find which subjects are the ones that are off. You can do this with something like fslview y.nii.gz where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit (you can mri_convert it to nii.gz). You can then step through each frame (or play them as a movie) to see if any look odd. The mincost is from the BBR cost function. It is basically the mean gray/white contrast across cortex passed through a sigmoid function to make its range 0-1, 0 being best. You cannot necessarily generalize the normal range for one modality to that of another. On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug et al., I indeed found 3 subjects, whose registration looked ok when I eyeballed them with the tkregister 2 command, with values of .9 and higher (all the other subjects had values between .44 and .61). Do you recommend to redo the analysis without them or to run the first level analysis again with --init-spm instead of --init-fsl in bbregister? Also, how is the first value in the .mincost file generated and what does it mean? Can you use this file for other modalities, too? Let's say if I want to do the first level analysis for fct. connectivity instead of PASL for example? Thanks, Rick 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: Wednesday, March 11, 2015 6:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation For the range, lower is better, but it impossible to say exactly what is good enough because it depends on your data. If it is 0.8 or higher, then that is probably bad. What I'm hoping is that there will be one or two outliers. The --init-spm was in place of --init-fsl in bbregister. But you only need that if you find a bad registration. On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote: I checked registration before and it was fine. However, I'll go back and look at the first value in the aslcal.reg.mincost file. What is the normal range? Also, I don't understand what you mean with the FSL initialization fails and try --init-spm - can you please give me some more information? Thanks! 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: Wednesday, March 11, 2015 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Try checking the individual registrations (or look at the first value in the .mincost file) to find subjects whose registration may have been off and so causes the final mask to be non-sense. Sometimes the FSL initialization fails. If so, you might try it with --init-spm On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote: Oh, I see what you mean. I accidentally sent you the within group analysis script. I am attaching the first level analysis script now. I also labeled the different steps to simplify the script a little bit. 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: Wednesday, March 11, 2015 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I still can't really tell what it is doing. It looks like it is just concatenating several input files that are passed on the command line. how were those created? On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote: Sure. I simplified it and attached it again. Please let me know if this is helpful! 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: Wednesday, March 11, 2015 3:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Sorry, I don't have time to deconstruct that script. Can you simplify it for me? On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote: This is the script I am using to create cbf.talaraich.mgz (attached). Thanks, Rick 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: Wednesday, March 11, 2015 3:22 PM To:
Re: [Freesurfer] Monte Carlo Simulation
Hi Doug et al., I indeed found 3 subjects, whose registration looked ok when I eyeballed them with the tkregister 2 command, with values of .9 and higher (all the other subjects had values between .44 and .61). Do you recommend to redo the analysis without them or to run the first level analysis again with --init-spm instead of --init-fsl in bbregister? Also, how is the first value in the .mincost file generated and what does it mean? Can you use this file for other modalities, too? Let's say if I want to do the first level analysis for fct. connectivity instead of PASL for example? Thanks, Rick 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: Wednesday, March 11, 2015 6:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation For the range, lower is better, but it impossible to say exactly what is good enough because it depends on your data. If it is 0.8 or higher, then that is probably bad. What I'm hoping is that there will be one or two outliers. The --init-spm was in place of --init-fsl in bbregister. But you only need that if you find a bad registration. On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote: I checked registration before and it was fine. However, I'll go back and look at the first value in the aslcal.reg.mincost file. What is the normal range? Also, I don't understand what you mean with the FSL initialization fails and try --init-spm - can you please give me some more information? Thanks! 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: Wednesday, March 11, 2015 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Try checking the individual registrations (or look at the first value in the .mincost file) to find subjects whose registration may have been off and so causes the final mask to be non-sense. Sometimes the FSL initialization fails. If so, you might try it with --init-spm On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote: Oh, I see what you mean. I accidentally sent you the within group analysis script. I am attaching the first level analysis script now. I also labeled the different steps to simplify the script a little bit. 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: Wednesday, March 11, 2015 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I still can't really tell what it is doing. It looks like it is just concatenating several input files that are passed on the command line. how were those created? On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote: Sure. I simplified it and attached it again. Please let me know if this is helpful! 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: Wednesday, March 11, 2015 3:36 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Sorry, I don't have time to deconstruct that script. Can you simplify it for me? On 03/11/2015 03:32 PM, Wolthusen, Rick Peter Fritz wrote: This is the script I am using to create cbf.talaraich.mgz (attached). Thanks, Rick 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: Wednesday, March 11, 2015 3:22 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Something went very wrong with your first level analysis because the final mask is pretty messed up. how did you create cbf.talairach.mgz ? On 03/11/2015 03:13 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug et al., Here is the glmdir file you were requesting: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1vzzxqva928 Thanks, Rick From: Wolthusen, Rick Peter Fritz Sent: Tuesday, March 10, 2015 2:10 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: RE: Monte Carlo Simulation Hi FS Community, I emailed with Doug a week ago with regards to limiting the results of a PASL Regression analysis to subcortical areas only in the tal output file (see below). I redid the analysis from scratch adding the flag --mask $SUBJECTS_DIR/fsaverage/mri.2mm/brainmask.mgz and after performing the Monte-Carlo Simulation (MCS), the .sig.cluster.summary file also refers to the above mentioned mask with regards to the used Mask Vol..
Re: [Freesurfer] Tracula: missing or incomplete tracts
Dear Anastasia, I was wondering if there is a way to automatically (in command line) derive the FA/V1 vector image. fslview FA.nii.gz V1.nii.gz allows to load the FA and V1 image, but then manual section of the (lines) is needed. freeview -dti V1 FA does it too (with different xyz convention), but the 'display as vectors' needs to be manually checked. Is there any way to produce this image using command line only? Thanks a lot!! Amelia -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Anastasia Yendiki Sent: Friday, March 06, 2015 6:56 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula: missing or incomplete tracts Hi Eileen - It looks like there was a A-P flip introduced to your gradient vectors. (See screenshot of the tensor eigenvectors. Because they look right in the coronal view but wrong in the sagittal and axial views, that's why I'm assuming the flip is in the A-P direction.) To fix this you need to multiply the y coordinate of your gradient vectors with -1 and rerun. If there are still any cases of missing tracts, please look at the bottom of your dmrirc file for instructions on how to use the reinit parameter (or search for previous emails on that parameter in the archives). Note that your DWI voxel size is anisotropic (finer resolution in x/y than z), this may cause bias in tractography, so I'd recommend that you switch to isotropic resolution for future acquisitions if you have control over it. Hope this helps, a.y On Fri, 27 Feb 2015, Eileen Moore wrote: Hi Anastasia, Sorry for the delay -- I missed your response. I did look at the anatomical segmentations and thought they looked OK. I've uploaded the tracula and corresponding freesurfer data for two subjects: one with complete tracts and one with missing/incomplete tracts. I also uploaded my dmrirc file. Thanks for taking a look for me. Eileen. Hi Eileen - Have you checked the anatomical segmentations of the subjects? The mask that's used by default is the aparc+aseg_mask, which comes from registering the cortical parcellationg and subcortical segmentation from T1 to diffusion space, and then dilating it by a couple of voxels. If you upload an example data set for me here, I can take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Please include all tracula-related directories of the subject (dmri, dlabel, etc). Thanks! a.y On Thu, 18 Dec 2014, Eileen Moore wrote: Hi - I'm having difficulty with missing or incomplete tracts most of my subjects. I'm hoping for suggestions on where I can look for data problems. The majority of my subjects have at least one missing/incomplete tract, but the specific problematic tract varies across subjects (e.g., one subject has a missing L.Uncinate; another subject has a missing Forceps Major; another is missing the ILF bilaterally, etc.). For my problematic tracts, the path.pd.nii.gz is a single line/curve rather than the diffuse volumetric distribution. I'm not sure how to correct this. I have checked my eigenvectors -- the lines appear to be pointing in the correct directions in my dtifit_V1 -- so I believe my gradient table is correct I've checked my images for motion via visual inspection and by excluding any subjects with dwi_motion outliers in AvgTranslation, AvgRotation, PercentBadSlices, and AvgDropoutScore. I inspected the nodif_brain_mask.nii.gz to look for chunks of missing brain and did not identify any problems here. I've tried increasing the number of control points for each tract. I'd very much appreciate any suggestions on how to troubleshoot next. Thank you, Eileen. ___ 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] newbie questions: transform RAS vectors to talaraich vectors and view
Thanks for getting back so quickly and for the clear answers. I was able to get the axial slices out by using mri_convert --split to create a .nii file. ImageJ could read that in and reslice it. Thanks again. Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, March 12, 2015 11:27 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] newbie questions: transform RAS vectors to talaraich vectors and view On 03/12/2015 09:54 AM, Krieger, Donald N. wrote: Dear List, I have sets of vectors in RAS coordinates from many volunteers. I want to transform them into coordinates for a standard volume. (1) I presume the standard volume that makes sense to use is orig.mgz in $FREESURFER_HOME/subjects/fsaverage/mri. Please confirm. Yes (2)I presume that I can transform the vectors contained in subject N's .label files to talairaich coordinates using the transform in $FREESURFER_HOME/subjects/subjectN/mri/transforms/talairach.xfm. Please confirm. Yes, though it is not easy to apply yourself. If you put the xyz into a label file, then you can use mri_label2label. Note that the xyz have to be in an FS coordinate system. See http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems (3)What tool can I use to convert orig.mgz into a sequence of axial cuts in some standard graphics format, e.g. gif, png, tiff? I don't know of one. Thanks and best regards, Don Signature0001 Don Krieger, Ph.D. Department of Neurological Surgery Universityof Pittsburgh ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Help with optseq2
The psdwin controls the window over which HRF overlap correction needs to be done. This is usually something like 0-22 sec, enough time for the HRF to return to baseline. If you want to set the minimum/maximum ITI, then use --tnullmin and --tnullmax doug On 03/11/2015 08:08 PM, Michael T Compton wrote: Hi, I am getting a unexpected result when I am running optseq2 and I don’t know if it is something I am not understanding correctly or if something else is going on. It is with ITI times. If I understand correctly the psdwin I entered below should return a min time of 4 and a max of 10, but I am getting values from 2 to as high as 24. Everything else is as expected, I hope you can help clear this up for me. Below is the info on my system and what I entered and attached is the log file and a couple of example outputs. Optseq2 version: ProgramName: optseq2 ProgramArguments: --all-info --all-info ProgramVersion: $Name: $ TimeStamp: 2015/03/11-22:47:23-GMT BuildTimeStamp: Sep 15 2009 21:37:45 CVS: $Id: optseq2.c,v 2.15 2009/05/26 18:13:45 greve Exp $ User: michaelcompton Machine: Michaels-MacBook-Pro.local Platform: Darwin PlatformVersion: 14.1.0 CompilerName: GCC CompilerVersion: 4 OS: Mac Yosemite 10.10.2 Here is what I am entering: ./optseq2 --ntp 168 --tr 2 --psdwin 4 10 2 --ev real 2 20 --ev photo 2 20 --nkeep 10 --o try111 --nsearch 10 Any help would be greatly appreciated, Michael Compton ___ 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] GLM analysis on CBF maps
Hello,
I have run GLM group analyses with Freesurfer tools according DODS model,
with six classes ((Male,Female) ; (Control,Left,Right)) and one age
variable :
*Class MaleControlClass MaleLeftClass MaleRightClass FemaleControlClass
FemaleLeftClass FemaleRightVariables Age *
I wanted to test *Control Left* and *Control Right* on CBF maps. I
defined with help of the tutorial contrats for that :
*control-left.intercept.mtx : 0.5 -0.5 0 0.5 -0.5 0 0 0 0 0 0
0control-left.slope.mtx : 0 0 0 0 0 0 0.5 -0.5 0 0.5 -0.5
0control-right.intercept.mtx : 0.5 0 -0.5 0.5 0 -0.5 0 0 0 0 0
0control-right.slope.mtx : 0 0 0 0 0 0 0.5 0 -0.5 0.5 0 -0.5*
My problem is that I don't know how to interpret significative results in
both *Control Left *contrasts* : **control-left.intercept.mtx *and
*control-left.slope.mtx.
*The same for* Control Right.* One is coding for intercept and the other
for slope, but concretely what significative results in both contrasts mean
?
Thank you in advance for helping !
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
2015-03-11 16:51 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:
the sig value is actually -log10(p)*sign(gamma) where gamma is the
contrast (gamma.mgh). The p-value is two-tailed, and the color indicates
what tail you are on.
doug
On 03/10/2015 01:21 PM, Matthieu Vanhoutte wrote:
Dear FreeSurfer's experts,
I have launched a GLM analyses following the tutorial :
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
Below the command I have used :
/mri_glmfit \
--y
${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.all.subjects.fwhm3.fsaverage.cbf_s.mgh
\
--fsgd ${FS_DIR}/SurfaceAnalysis_mri_glmfit/g6v1.fsgd dods \
--C ${FS_DIR}/SurfaceAnalysis_mri_glmfit/control-left.intercept.mtx \
--surf fsaverage lh \
--cortex \
--glmdir ${FS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/
In order to see the uncorrected results with p.0001, I ran :
/freeview -f
${SUBJECTS_DIR}/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=${SUBJECTS_DIR}/SurfaceAnalysis_mri_glmfit/lh.g6v1.glmdir/control-left.intercept/sig.mgh:overlay_threshold=4,5
-viewport 3d/
However, nothing appears with this threshold and when I wanted to
configure overlay I saw that most of my values in /sig.mgh /were
negatives between -4 and 0...
How is possible for /-log10(pvalue)/ values ? Could I obtain
significant uncorrected values from this /sig.mgh/ file ?
Please find attached my needed files : *y.fsgd, mri_glmfit.log,
**/control-left.intercept.mtx/ and sig.mgh *
Thank you in advance for helping me !!
Best regards,
-
Matthieu Vanhoutte, MSc
Research Engineer - Department of Neuroradiology
Regional University Hospital, Lille, France
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--
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/
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The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
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Re: [Freesurfer] Monte Carlo Simulation
To be honest, I checked the between subject alignment and it looked pretty good. None of my subjects was way out of alignment. However, since we cannot fit the whole brain in the slice during scanning, we are always cutting of the top of the brain, sometimes more, sometimes less, depending on the brain size. Could this be the reason why the mask is off? If not, is there anything else I can check? 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: Thursday, March 12, 2015 2:47 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I meant which ones are causing the problems when you run mri_glmfit. When you run fslview you will see something that looks like a brain. As you scroll thru the different time points, you'll see the CBF maps for different subjects. They should be more-or-less in alignment. Look for ones that are way out of alignment or don't have all of the brain. On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote: Well, I checked the proper match of ASL and anatomical scans again and one of the subjects I reported before was indeed wrongly matched. Thanks! What do you mean with So the next thing I would do is to find which subjects are the ones that are off.? You mean off when I check for registration? That's what I did before with tkregister2 and they all looked fine to me. What do I look for when I open the cbf.talaraich.nii.gz file in fslview? 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: Thursday, March 12, 2015 12:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation If the registration looks ok, then that is all that counts. However, I'm a bit sceptical that the reg looks ok but the mincost is that much different than the others. You should double check that the ASL is properly matched with the corresponding anatomical (ie, it is not two different subjects). This would also not explain why the masks were so far off. So the next thing I would do is to find which subjects are the ones that are off. You can do this with something like fslview y.nii.gz where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit (you can mri_convert it to nii.gz). You can then step through each frame (or play them as a movie) to see if any look odd. The mincost is from the BBR cost function. It is basically the mean gray/white contrast across cortex passed through a sigmoid function to make its range 0-1, 0 being best. You cannot necessarily generalize the normal range for one modality to that of another. On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug et al., I indeed found 3 subjects, whose registration looked ok when I eyeballed them with the tkregister 2 command, with values of .9 and higher (all the other subjects had values between .44 and .61). Do you recommend to redo the analysis without them or to run the first level analysis again with --init-spm instead of --init-fsl in bbregister? Also, how is the first value in the .mincost file generated and what does it mean? Can you use this file for other modalities, too? Let's say if I want to do the first level analysis for fct. connectivity instead of PASL for example? Thanks, Rick 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: Wednesday, March 11, 2015 6:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation For the range, lower is better, but it impossible to say exactly what is good enough because it depends on your data. If it is 0.8 or higher, then that is probably bad. What I'm hoping is that there will be one or two outliers. The --init-spm was in place of --init-fsl in bbregister. But you only need that if you find a bad registration. On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote: I checked registration before and it was fine. However, I'll go back and look at the first value in the aslcal.reg.mincost file. What is the normal range? Also, I don't understand what you mean with the FSL initialization fails and try --init-spm - can you please give me some more information? Thanks! 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: Wednesday, March 11, 2015 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Try checking the individual registrations (or look at the first value in the .mincost file) to
Re: [Freesurfer] newbie questions: transform RAS vectors to talaraich vectors and view
On 03/12/2015 09:54 AM, Krieger, Donald N. wrote: Dear List, I have sets of vectors in RAS coordinates from many volunteers. I want to transform them into coordinates for a standard volume. (1) I presume the standard volume that makes sense to use is orig.mgz in $FREESURFER_HOME/subjects/fsaverage/mri. Please confirm. Yes (2)I presume that I can transform the vectors contained in subject N’s .label files to talairaich coordinates using the transform in $FREESURFER_HOME/subjects/subjectN/mri/transforms/talairach.xfm. Please confirm. Yes, though it is not easy to apply yourself. If you put the xyz into a label file, then you can use mri_label2label. Note that the xyz have to be in an FS coordinate system. See http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems (3)What tool can I use to convert orig.mgz into a sequence of axial cuts in some standard graphics format, e.g. gif, png, tiff? I don't know of one. Thanks and best regards, Don Signature0001 Don Krieger, Ph.D. Department of Neurological Surgery Universityof Pittsburgh ___ 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] follow up and double check: transform RAS vectors to talaraich
what do you want us to check? On 03/12/2015 03:27 PM, Krieger, Donald N. wrote: Dear List, I’ve done a couple of spot checks which appear to work but want to double check with you. Attached are 5 axial cuts from fsaverage’s orig.mgz 5 mm apart. The “white” surface vectors are shown in black for lh.postcentral. I also put all of the CC vectors from the aseg; these show on the lower 3 cuts. I’ve also put in red and green the lh.postcentral “white” surface vectors from two of my scans. What do you think? Regards, Don Signature0001 Don Krieger, Ph.D. Department of Neurological Surgery Universityof Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text ___ 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] follow up and double check: transform RAS vectors to talaraich
Do the results in the attached images make sense? Does it make sense that the transformation was obtained: mri_info --vox2ras-fls ? Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, March 12, 2015 3:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich what do you want us to check? On 03/12/2015 03:27 PM, Krieger, Donald N. wrote: Dear List, I've done a couple of spot checks which appear to work but want to double check with you. Attached are 5 axial cuts from fsaverage's orig.mgz 5 mm apart. The white surface vectors are shown in black for lh.postcentral. I also put all of the CC vectors from the aseg; these show on the lower 3 cuts. I've also put in red and green the lh.postcentral white surface vectors from two of my scans. What do you think? Regards, Don Signature0001 Don Krieger, Ph.D. Department of Neurological Surgery Universityof Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich
I forget to include that the transform I used was obtained: mri_info aseg.mgz -vox2ras-fsl Regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N. Sent: Thursday, March 12, 2015 3:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] follow up and double check: transform RAS vectors to talaraich Dear List, I've done a couple of spot checks which appear to work but want to double check with you. Attached are 5 axial cuts from fsaverage's orig.mgz 5 mm apart. The white surface vectors are shown in black for lh.postcentral. I also put all of the CC vectors from the aseg; these show on the lower 3 cuts. I've also put in red and green the lh.postcentral white surface vectors from two of my scans. What do you think? Regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text ___ 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] follow up and double check: transform RAS vectors to talaraich
sorry, I don't know what you've done or what you are trying to do or what the mri_info command is related to. Can you fill in the details? On 03/12/2015 04:20 PM, Krieger, Donald N. wrote: Do the results in the attached images make sense? Does it make sense that the transformation was obtained: mri_info --vox2ras-fls ? Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, March 12, 2015 3:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] follow up and double check: transform RAS vectors to talaraich what do you want us to check? On 03/12/2015 03:27 PM, Krieger, Donald N. wrote: Dear List, I've done a couple of spot checks which appear to work but want to double check with you. Attached are 5 axial cuts from fsaverage's orig.mgz 5 mm apart. The white surface vectors are shown in black for lh.postcentral. I also put all of the CC vectors from the aseg; these show on the lower 3 cuts. I've also put in red and green the lh.postcentral white surface vectors from two of my scans. What do you think? Regards, Don Signature0001 Don Krieger, Ph.D. Department of Neurological Surgery Universityof Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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] Monte Carlo Simulation
I meant which ones are causing the problems when you run mri_glmfit. When you run fslview you will see something that looks like a brain. As you scroll thru the different time points, you'll see the CBF maps for different subjects. They should be more-or-less in alignment. Look for ones that are way out of alignment or don't have all of the brain. On 03/12/2015 02:35 PM, Wolthusen, Rick Peter Fritz wrote: Well, I checked the proper match of ASL and anatomical scans again and one of the subjects I reported before was indeed wrongly matched. Thanks! What do you mean with So the next thing I would do is to find which subjects are the ones that are off.? You mean off when I check for registration? That's what I did before with tkregister2 and they all looked fine to me. What do I look for when I open the cbf.talaraich.nii.gz file in fslview? 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: Thursday, March 12, 2015 12:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation If the registration looks ok, then that is all that counts. However, I'm a bit sceptical that the reg looks ok but the mincost is that much different than the others. You should double check that the ASL is properly matched with the corresponding anatomical (ie, it is not two different subjects). This would also not explain why the masks were so far off. So the next thing I would do is to find which subjects are the ones that are off. You can do this with something like fslview y.nii.gz where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit (you can mri_convert it to nii.gz). You can then step through each frame (or play them as a movie) to see if any look odd. The mincost is from the BBR cost function. It is basically the mean gray/white contrast across cortex passed through a sigmoid function to make its range 0-1, 0 being best. You cannot necessarily generalize the normal range for one modality to that of another. On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug et al., I indeed found 3 subjects, whose registration looked ok when I eyeballed them with the tkregister 2 command, with values of .9 and higher (all the other subjects had values between .44 and .61). Do you recommend to redo the analysis without them or to run the first level analysis again with --init-spm instead of --init-fsl in bbregister? Also, how is the first value in the .mincost file generated and what does it mean? Can you use this file for other modalities, too? Let's say if I want to do the first level analysis for fct. connectivity instead of PASL for example? Thanks, Rick 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: Wednesday, March 11, 2015 6:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation For the range, lower is better, but it impossible to say exactly what is good enough because it depends on your data. If it is 0.8 or higher, then that is probably bad. What I'm hoping is that there will be one or two outliers. The --init-spm was in place of --init-fsl in bbregister. But you only need that if you find a bad registration. On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote: I checked registration before and it was fine. However, I'll go back and look at the first value in the aslcal.reg.mincost file. What is the normal range? Also, I don't understand what you mean with the FSL initialization fails and try --init-spm - can you please give me some more information? Thanks! 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: Wednesday, March 11, 2015 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Try checking the individual registrations (or look at the first value in the .mincost file) to find subjects whose registration may have been off and so causes the final mask to be non-sense. Sometimes the FSL initialization fails. If so, you might try it with --init-spm On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote: Oh, I see what you mean. I accidentally sent you the within group analysis script. I am attaching the first level analysis script now. I also labeled the different steps to simplify the script a little bit. 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: Wednesday, March 11, 2015 4:50 PM To:
Re: [Freesurfer] Monte Carlo Simulation
Well, I checked the proper match of ASL and anatomical scans again and one of the subjects I reported before was indeed wrongly matched. Thanks! What do you mean with So the next thing I would do is to find which subjects are the ones that are off.? You mean off when I check for registration? That's what I did before with tkregister2 and they all looked fine to me. What do I look for when I open the cbf.talaraich.nii.gz file in fslview? 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: Thursday, March 12, 2015 12:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation If the registration looks ok, then that is all that counts. However, I'm a bit sceptical that the reg looks ok but the mincost is that much different than the others. You should double check that the ASL is properly matched with the corresponding anatomical (ie, it is not two different subjects). This would also not explain why the masks were so far off. So the next thing I would do is to find which subjects are the ones that are off. You can do this with something like fslview y.nii.gz where y.nii.gz is the stack of cpf maps that you passed to mri_glmfit (you can mri_convert it to nii.gz). You can then step through each frame (or play them as a movie) to see if any look odd. The mincost is from the BBR cost function. It is basically the mean gray/white contrast across cortex passed through a sigmoid function to make its range 0-1, 0 being best. You cannot necessarily generalize the normal range for one modality to that of another. On 03/12/2015 12:11 PM, Wolthusen, Rick Peter Fritz wrote: Hi Doug et al., I indeed found 3 subjects, whose registration looked ok when I eyeballed them with the tkregister 2 command, with values of .9 and higher (all the other subjects had values between .44 and .61). Do you recommend to redo the analysis without them or to run the first level analysis again with --init-spm instead of --init-fsl in bbregister? Also, how is the first value in the .mincost file generated and what does it mean? Can you use this file for other modalities, too? Let's say if I want to do the first level analysis for fct. connectivity instead of PASL for example? Thanks, Rick 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: Wednesday, March 11, 2015 6:34 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation For the range, lower is better, but it impossible to say exactly what is good enough because it depends on your data. If it is 0.8 or higher, then that is probably bad. What I'm hoping is that there will be one or two outliers. The --init-spm was in place of --init-fsl in bbregister. But you only need that if you find a bad registration. On 03/11/2015 05:30 PM, Wolthusen, Rick Peter Fritz wrote: I checked registration before and it was fine. However, I'll go back and look at the first value in the aslcal.reg.mincost file. What is the normal range? Also, I don't understand what you mean with the FSL initialization fails and try --init-spm - can you please give me some more information? Thanks! 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: Wednesday, March 11, 2015 5:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation Try checking the individual registrations (or look at the first value in the .mincost file) to find subjects whose registration may have been off and so causes the final mask to be non-sense. Sometimes the FSL initialization fails. If so, you might try it with --init-spm On 03/11/2015 05:15 PM, Wolthusen, Rick Peter Fritz wrote: Oh, I see what you mean. I accidentally sent you the within group analysis script. I am attaching the first level analysis script now. I also labeled the different steps to simplify the script a little bit. 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: Wednesday, March 11, 2015 4:50 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Monte Carlo Simulation I still can't really tell what it is doing. It looks like it is just concatenating several input files that are passed on the command line. how were those created? On 03/11/2015 03:54 PM, Wolthusen, Rick Peter Fritz wrote: Sure. I simplified it and attached it again. Please let me know if this is helpful! From:
Re: [Freesurfer] Which files are needed to run longitudinal analysis?
Sorry, I believe I have fixed this by using --surface fsaverage lh. Thanks, Kate On Fri, Mar 13, 2015 at 9:59 AM, Kate Riggall kate.rigg...@gmail.com wrote: Bruce and Martin, Thanks, I now have it running of an external hard drive and it is working well. As a follow-up question: When I run the paired analysis, the final command (mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --C age.mtx) returns ERROR: you must use '--surface subject hemi' with surface data. I can add that flag easily, but I am not sure what to put in the 'subject' spot, as I am looking at not one subject but rather a large group. Also, given that I am running a two time point analysis, is it sufficient to put the original subject names in the FSGD files, or should I specify subject.long to use the longitudinally processed data? Cheers, Kate Riggall On Thu, Mar 12, 2015 at 12:01 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Kate, if you are only running stats on the longitudinally processed dirs, it should be sufficient to copy only the *.long.* directories and the base directories. You can skip the cross sectionals. If you do an LME, you can probably also skip the base dirs. But you'd need them for the 2-stage stats approach. Best, Martin On 03/10/2015 05:38 AM, Kate Riggall wrote: Hello, I am trying to run a paired analysis (a two time-point longitudinal analysis) on some subjects which have been longitudinally pre-processed for me on another computer. The computer I am now working on is originally a Windows computer, but is now running Linux on a partition (CentOS Release 6.6, Kernel Linux 2.6, GNOME 2.28.2). I have been advised by my IT staff to copy the files I need onto the linux partition to avoid any issues with accessing external/share drives. My subjects folder is 63 GB, which is a bit big to fit on the partition, so I am wondering if I can copy over just the files needed for the analysis step, and what those files would be. Thanks in advance, Kate Riggall ___ 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 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] eTIV, mri_label_volume, and scale factor
Hi, I am trying to eTIV correct the volumetric stats output from recon-all (ie aseg stats and aparc stats). I read the eTIV-estimated Total Instranial Volume, aka ICV wiki information, but I still have some questions. 1. Do all structures need to be eTIV corrected? 2. To use mri_label_volume, it looks like I will need a scale factor. Where do I find this scale factor? I assume it is different for each brain. 3. The output of mri_label_volume seems to be a percentage of the eTIV volume, so, in theory should the total percentages of all structures add up to one? Do most people analyze these percentage outputs or is this a step towards the actual data that is then analyzed? Thanks! Colleen ___ 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] Which files are needed to run longitudinal analysis?
Bruce and Martin, Thanks, I now have it running of an external hard drive and it is working well. As a follow-up question: When I run the paired analysis, the final command (mri_glmfit --glmdir lh.paired-diff --y lh.paired-diff.thickness.sm05.mgh --fsgd paired-diff.fsgd --C mean.mtx --C age.mtx) returns ERROR: you must use '--surface subject hemi' with surface data. I can add that flag easily, but I am not sure what to put in the 'subject' spot, as I am looking at not one subject but rather a large group. Also, given that I am running a two time point analysis, is it sufficient to put the original subject names in the FSGD files, or should I specify subject.long to use the longitudinally processed data? Cheers, Kate Riggall On Thu, Mar 12, 2015 at 12:01 AM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Kate, if you are only running stats on the longitudinally processed dirs, it should be sufficient to copy only the *.long.* directories and the base directories. You can skip the cross sectionals. If you do an LME, you can probably also skip the base dirs. But you'd need them for the 2-stage stats approach. Best, Martin On 03/10/2015 05:38 AM, Kate Riggall wrote: Hello, I am trying to run a paired analysis (a two time-point longitudinal analysis) on some subjects which have been longitudinally pre-processed for me on another computer. The computer I am now working on is originally a Windows computer, but is now running Linux on a partition (CentOS Release 6.6, Kernel Linux 2.6, GNOME 2.28.2). I have been advised by my IT staff to copy the files I need onto the linux partition to avoid any issues with accessing external/share drives. My subjects folder is 63 GB, which is a bit big to fit on the partition, so I am wondering if I can copy over just the files needed for the analysis step, and what those files would be. Thanks in advance, Kate Riggall ___ 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 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.
