[Freesurfer] average values per cluster
Dear Freesurfer experts, Sorry to bother you again, but I have two more questions about extracting (thickness/surface/GI) values from a certain cluster. As I understood, the abs.y.ocn.dat file gives the average values for a given significant cluster (e.g. a cluster where there is a significant AxB interaction). I may be completely misunderstanding things, but if I use these values in SPSS for further statistics and test the same interaction (AxB), than according to SPSS this interaction is not significant (corrected for the same covariates as in the FSGD file). Could you tell me what is going wrong here? I do not trust my results now. Furthermore, is it possible (and if so, how?) to extract the average values of exactly the same cluster, but in an independent group not used in the analysis, for post-hoc comparisons in SPSS? Thanks, Maaike___ 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] average values per cluster
We get these kind of reports occasionally. When I ask people to confirm
that they use exactly the same design matrix in SPSS, I never hear back,
so I assume that it gets resolved. So please check. The other thing you
can do is to run in matlab, something like
cd glmdir/contrast
X = load('Xg.dat');
y = load('ocn.dat');
C = load('C.dat');
[beta rvar] = fast_glmfit(y,X);
[F p] = fast_fratio(beta,X,rvar,C);
p will be the p-value
If you used an unsigned cluster-forming threshold (ie, abs), then it is
possible that some of the voxels are pos and some are neg so that they
average out
doug
On 01/26/2015 09:03 AM, maaike rive wrote:
Dear Freesurfer experts,
Sorry to bother you again, but I have two more questions about
extracting (thickness/surface/GI) values from a certain cluster.
As I understood, the abs.y.ocn.dat file gives the average values for a
given significant cluster (e.g. a cluster where there is a significant
AxB interaction).
I may be completely misunderstanding things, but if I use these values
in SPSS for further statistics and test the same interaction (AxB),
than according to SPSS this interaction is /not /significant
(corrected for the same covariates as in the FSGD file).
Could you tell me what is going wrong here? I do not trust my results now.
Furthermore, is it possible (and if so, how?) to extract the average
values of exactly the same cluster, but in an independent group not
used in the analysis, for post-hoc comparisons in SPSS?
Thanks,
Maaike
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Re: [Freesurfer] vertex-wise covariate for gyrification index
QDEC does not allow it, but you can do it with mri_glmfit with the --pvr option. Run mri_glmfit with --help to get more info. doug On 01/25/2015 11:16 AM, angela.fav...@unipd.it wrote: Hi all, I wrote a paper about gyrification in a sample of malnourished patients. I found only little overlap between maps of significantly rediced cortical thickness and maps of significantly reduced gyrification index (in comparison to a group of healthy controls). One of the reviewer raised the question that this is not sufficient to demonstrate that reduced gyrification is not due to reduced cortical thickness (or GM volume) and suggest to perform a between group analysis using cortical thickness (or volume) maps as vertex-wise covariates. Is it possible to perform this type of analysis? I believe that QDEC does not allow it Thank you Angela Hi Maria it's really hard to say - you'll need to try it out. There aren't strong prior constraints on skull shape, but if the shape of the brain is too different, things may degrade Bruce On Fri, 23 Jan 2015, Maria Holland wrote: Hi all, I am starting a project analyzing patients with cranial deformities. How robust is the automatic cortical reconstruction process - i.e., would it be able to handle deformed skulls? Similar to this picture: http://upload.wikimedia.org/wikipedia/commons/1/1f/Single_suture_synostosis .png I am also wondering about the possibility of getting information about the intermediate steps of the local gyrification calculation. Like, could we get information on the pial and outer pial surface paths on each individual slice, before that information is turned into a 3D surface? Thanks for your help! ~ Maria ___ 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] cortical thickness analysis
what is your mri_glmfit-sim command line? Try running it with --cwp 1 to get all clusters regardless of their p-value doug On 01/23/2015 04:01 PM, Hirsch, Gabriella wrote: Hi freesurfer experts, I have a question I was hoping someone could help me with; I am currently analysing the cortical thickness of two subject populations (patient and control) using the group analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng). However, when I ran the processing stream for the clusterwise correction for multiple comparisons, all my visualized clusters all disappeared (using tksurfer or freeview) and no clusters showed to be significant in the CWP column of the cluster summary txt file (NClusters=0). I have played around with the thresholds but it doesn't seem to make much of a difference. For what it's worth, I'm using a simple t-test contrast. Any thoughts as to what is going on? Similarly, is there any way of accessing p-values of uncorrected clusters? Thanks so much for your help. Best, 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] Some questions about fsaverage
You'll need to get a copy of mri_surf2surf.{linux,mac}. It was there all
the time I just did not put it on the installation page. I've updated
the page with this link
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/xhemi/mri_surf2surf.{linux,mac}
When you re-run delete the xhemi folder if it exists.
On 01/23/2015 12:32 PM, Alexandre Routier wrote:
Hello everyone,
I have a new question concerning fsaverage: I would like to perform
some asymmetry analyses but I noticed that the left and right
hemispheres were not symmetric.
I found here ( https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi ) how
to register a subject to fsaverage_sym but I have some issues.
surfreg --s $subject --t fsaverage_sym --lh worked fine (see first
log file) and the ${subject}/xhemi/surf/ folder is empty.
Then surfreg --s $subject --t fsaverage_sym --lh --xhemi (see second
log file) didn't work because ${subject}/xhemi/surf/lh.sphere was not
found. Did I miss something ? I modified FS 5.1 thanks to the section
Installation concerning my configuration.
Moreover, I cannot test yet but I would like to know if the following
commands will work for a single subject:
mris_preproc --target fsaverage_sym --hemi lh \
--xhemi --paired-diff \
--srcsurfreg fsaverage_sym.sphere.reg \
--meas thickness \
--out lh.lh-rh.thickness.sm00.mgh \
--s ${name_subject}
# Smooth e.g. 10mm of the surface
mris_fwhm --s ${name_subject} --hemi lh --cortex --smooth-only --fwhm
10 --i lh.lh-rh.thickness.sm00.mgh --o lh.lh-rh.thickness.sm10.mgh
# Analyze
mri_glmfit --y lh.lh-rh.thickness.sm10.mgh --glmdir
glm.lh.lh-rh.thickness.sm10 --osgm --surf ${name_subject} lh
I slightly modified the commands on the tutorial for my needs but I
can't check for the moment.
Thanks in advance for your help.
Best regards,
Alexandre
2014-12-05 12:09 GMT+01:00 Alexandre Routier
alexandre.rout...@gmail.com mailto:alexandre.rout...@gmail.com:
Hello,
Thanks for your answers :)
mri_annotation2label enabled me to convert the ROI of Desikan
Atlas as I wanted and the Brodmann were indeed in
$FREESURFER_HOME/subjects/fsaverage/label .
Have a nice day,
Alexandre
2014-12-04 23:01 GMT+01:00 Bruce Fischl
fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu:
Hi Alexandre
I'm not entirely sure what you are asking, but the fsaverage
Brodmann areas and parcellations should all be stored in the
directory:
$FREESURFER_HOME/subjects/fsaverage/label
cheers
Bruce
On Thu, 4 Dec 2014, Alexandre Routier wrote:
Hello,
I am currently working with cortical thickness and more
particularly with
the fsaverage. Since the thickness has the same number of
voxel, I would
like to correspond the voxels with some ROI, for instance the
Desikan-Killiany Atlas or the Brodmann area.
Are they any label or text files which correspond a ROI
with the indices of
the voxels in fsaverage ?
Thanks in advance for you help,
Alexandre
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Re: [Freesurfer] FREESURFER] ERROR: matrix is ill-conditioned or badly scaled, condno = 164365
Try demeaning your covariates. Do so on a sample-wise basis (ie, compute the mean age across all subjects, then subtract that mean from all ages) doug On 01/14/2015 07:30 PM, i_geschwind2013 wrote: /Hello/ /I’m trying to do an group analysis using mir_glmfit but I met this error./ ERROR: matrix is ill-conditioned or badly scaled, condno = 165279 1. my command line was mri_glmfit --y lh.age_edu.thickness.10b.mgh --fsgd age_edu.fsgd --C C_age.edu.mtx --surf fsaverage lh --cortex --glmdir lh.age_edu.glmdir 2. I attached the fsgd file, which was made in edit. It contains 1 class (2 levels) and 2 variables (age education) 3. contrast is ‘-1 1 0 0 0 0’ 4. design matrix is like below Design matrix -- 1.000 0.000 74.000 0.000 14.000 0.000; 1.000 0.000 70.000 0.000 12.000 0.000; 1.000 0.000 73.000 0.000 6.000 0.000; 1.000 0.000 84.000 0.000 15.000 0.000; 0.000 1.000 0.000 60.000 0.000 12.000; 0.000 1.000 0.000 59.000 0.000 12.000; 0.000 1.000 0.000 63.000 0.000 9.000; 0.000 1.000 0.000 60.000 0.000 12.000; ERROR: matrix is ill-conditioned or badly scaled, condno = 164365 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y lh.age_edu.thickness.10b.mgh --fsgd age_edu.fsgd --C C_age.edu.mtx --surf fsaverage lh --cortex --glmdir lh.age_edu.glmdir 2. The FSGD file (if using one) 3. And the design matrix above thanks, H.A. LEE ___ 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] mri_cnr and bash
Dear all,
I have come up with a pretty good preliminary solution namely:
I run the first loop that returns me CNR and some other stuff from the command
mri_cnr. It creates one txt. file for each subject.
for i in *3T; do mri_cnr $i/surf $i/mri/norm.mgz $i/$i_cnr.txt; done
(All of my subjects' names contain the expression 3T, so if someone would like
to use it, just adjust it properly)
The second loop gives me a single txt. file with the list of cnr value only
(that is 'total CNR'). However, without subjects ID. I couldnt figure it out
yet, how to do this.
for i in $(find . -name *cnr.txt); do awk 'NR==8 {print $4}' $i
cnr_sample.txt; done
But all in all, I would say the problem is more or less solved, so thanks
everybody for your input.
Cheers,
Jacek
gray/white CNR is the first column
On Thu, 22 Jan 2015, Jacek Manko wrote:
Dear Dr. Greve, dear Dr. Fischl
would something like this work?
set cnr = `mri_cnr $SUBJECTS_DIR/$subject/surf
$SUBJECTS_DIR/$subject/mri/norm.mgz | grep total | awk '{print $4}'`
echo $subject $cnr yourfile
Unfortunately it doesnt. I was trying to modify the paths, but got
always results like:
MRISread(/surf/lh.white): could not open file
No such file or directory
mri_cnr: could not read surface file /surf/lh.white
No such file or directory
and @Dr. Fischl
actually if you run mri_cnr with -l out.log it will write a line to
out.log
of the form:
gray_white_cnr gray_csf_cnr white_mean gray_mean csf_mean
sqrt(white_var) sqrt(gray_var) sqrt(csf_var))
so you would create one file for each subject. You could then run a for
loop over your subjects to cat them into a single file
Indeed, but I dont quite get it, how to extract CNR from these values.
Thanks,
Cheers,
Jacek Manko
On 01/21/2015 02:46 PM, Jacek Manko wrote:
My desirable output would be then a .txt file that consists of merely
two columns. The first column is the subject's ID and the second is the
CNR value only, for example:
bruce 1.602
bert 1.555
john_doe 1.666
Thanks in advance.
Cheers,
Jacek
Dnia 21-01-2015 o godz. 20:34 Bruce Fischl napisał(a):
Hi Jacek
if you give us an example of what the desired output would be for you it
would just be a couple of minutes to put it in the code. Or maybe someone
can post some sed code (or some easy alternative) to parse the CNR out of
the output.
Bruce
On Wed,
21 Jan 2015, Jacek Manko wrote:
Oh, I thought it was already defined. I am referring actually to this
thread...
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-August/025251.html
...and, allowing myself to specify my problem, when I type the command
'mri_cnr' what I become in my terminal is something more or less like
that:
mri_cnr ~/local_subjects/bruce/surf
~/local_subjects/bruce/mri/norm.mgz
processing MRI volume
/homes/4/fischl/local_subjects/bruce/mri/norm.mgz...
white = 95.8+-9.7, gray = 65.3+-17.9, csf = 40.1+-17.2
gray/white CNR = 2.241, gray/csf CNR = 1.026
lh CNR = 1.633
white = 95.7+-9.9, gray = 65.5+-17.8, csf = 41.5+-17.4
gray/white CNR = 2.205, gray/csf CNR = 0.937
rh CNR = 1.571
total CNR = 1.602
My question is, if there is a way to export the CNR value, that is
1.602, to a seperate file alongside with the subject's ID. I suppose
there are no such bulit-in commands in FreeSurfer, is that right?
Thanks.
Cheers,
Jacek Manko
Dnia 21-01-2015 o godz. 18:38 Douglas N Greve napisał(a):
how do you want to define CNR?
On 01/21/2015 06:21 AM, Jacek Manko wrote:
Dear All,
I have been wondering if there is a way (already implemented in the
FreeSurfer) to export CNR measurement outputs to seperate file, like a
table or someting. If not, it will possible only via some pretty
advanced bash scripting, am I right? If so, has anyone some experience
with that matter?
Thanks.
Cheers,
Jacek Manko
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[Freesurfer] extracting pvalues
Hi FreeSurfer experts, Is there a way to extract significant pvalues from sig.mgh files (Obtained from the GroupAnalysisDng tutorial)? I've looked online but having trouble. Somehow mris_covert isn't working. Thanks! Gabriella ___ 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] vertex-wise covariate for gyrification index
Hi Doug, thank you for this hint. I have included --pvr in my mri_glmfit command using a stack of cortical thickness maps of the same hemisphere (and same subjects in the same order). I also added a column in my design matrix. It seems to work. Only when I use the mri_glmfit-sim command, this message appears: WARNING: unrecognized mri_glmfit cmd option --pvr WARNING: unrecognized mri_glmfit cmd option /qdec/lh_LGI_vtw/thick.mgh but everything seems to work anyway (and clusters of differences do not disappear!!). Is it all correct? Thank you for your help! Angela QDEC does not allow it, but you can do it with mri_glmfit with the --pvr option. Run mri_glmfit with --help to get more info. doug On 01/25/2015 11:16 AM, angela.fav...@unipd.it wrote: Hi all, I wrote a paper about gyrification in a sample of malnourished patients. I found only little overlap between maps of significantly rediced cortical thickness and maps of significantly reduced gyrification index (in comparison to a group of healthy controls). One of the reviewer raised the question that this is not sufficient to demonstrate that reduced gyrification is not due to reduced cortical thickness (or GM volume) and suggest to perform a between group analysis using cortical thickness (or volume) maps as vertex-wise covariates. Is it possible to perform this type of analysis? I believe that QDEC does not allow it Thank you Angela Hi Maria it's really hard to say - you'll need to try it out. There aren't strong prior constraints on skull shape, but if the shape of the brain is too different, things may degrade Bruce On Fri, 23 Jan 2015, Maria Holland wrote: Hi all, I am starting a project analyzing patients with cranial deformities. How robust is the automatic cortical reconstruction process - i.e., would it be able to handle deformed skulls? Similar to this picture: http://upload.wikimedia.org/wikipedia/commons/1/1f/Single_suture_synostosis .png I am also wondering about the possibility of getting information about the intermediate steps of the local gyrification calculation. Like, could we get information on the pial and outer pial surface paths on each individual slice, before that information is turned into a 3D surface? Thanks for your help! ~ Maria ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Extract mean time series from parcellated region
Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold# mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz# mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka___ 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] Extraction of T2 map statistics-per-segment
Hello — I’m trying to extract quantitative T2 values for different brain segments. I’ve converted my T2 set of DICOMs to .mgz format using mri_convert and loaded them into freeview. mri_convert -it siemens_dicom -ot mgz T2_maps_Dir/slice_1_T2_map.dcm T2_in_mgz.mgz After loading T2_in_mgz.mgz to Freeview the T2 maps seem to coincide very well with the segmentation maps (aseg+aparc-in-rawavg.mgz). My questions are: 1. Should I have applied some pre-registration operation on the T2 maps before loading them into freeview, or does the fact that they coincide with the segmentation maps mean that I don’t need to apply any registration? 2. How can I extract mean T2 values for different segments? (not the usual volume-per-segment) Much obliged! — Noam -- Noam Ben-Eliezer, PhD Adjunct Assistant Professor of Radiology Center for Biomedical-Imaging New-York University Medical School noam.ben-elie...@nyumc.orgmailto:noam.ben-elie...@nyumc.org ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] extracting pvalues
what do you mean? Just a list of values? the column, row, slice as well? On 1/26/15 4:02 PM, Hirsch, Gabriella wrote: Hi FreeSurfer experts, Is there a way to extract significant pvalues from sig.mgh files (Obtained from the GroupAnalysisDng tutorial)? I've looked online but having trouble. Somehow mris_covert isn't working. Thanks! 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] Extract mean time series from parcellated region
what do you mean you can't get them? The program fails? It produces 0s? On 1/26/15 3:48 PM, sabin khadka wrote: Hi FS user, I am trying to extract time series of fmri rest data of certain parcellated regions (both cortical and subcortical). for that I am doing following # bbregister --s sub id --mov EPI.nii.gz --init-fsl --reg register.dat --bold # mri_label2vol --aparc+aseg --subject sub id --temp EPI.nii.gz --fillthresh 0.5 --reg regsiter.dat --o test1.nii.gz # mri_vol2vol --mov test1.nii.gz --targ sub id/mri/aparc+aseg.mgz --reg register.dat --o test2.nii.gz # mri_segstats --seg sub id/mri/aparc+aseg.mgz --id e.g. 11 for L caudate --in test2.nii.gz --avgwf textfile.txt I am not able to get the mean time series values. Could anyone tell me what I am missing? Cheers, Sabin Khadka ___ 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] vertex-wise covariate for gyrification index
That's fine. mri_glmfit-sim has a little anxiety when it finds mri_glmfit options it does not recognize. doug On 1/26/15 5:00 PM, angela.fav...@unipd.it wrote: Hi Doug, thank you for this hint. I have included --pvr in my mri_glmfit command using a stack of cortical thickness maps of the same hemisphere (and same subjects in the same order). I also added a column in my design matrix. It seems to work. Only when I use the mri_glmfit-sim command, this message appears: WARNING: unrecognized mri_glmfit cmd option --pvr WARNING: unrecognized mri_glmfit cmd option /qdec/lh_LGI_vtw/thick.mgh but everything seems to work anyway (and clusters of differences do not disappear!!). Is it all correct? Thank you for your help! Angela QDEC does not allow it, but you can do it with mri_glmfit with the --pvr option. Run mri_glmfit with --help to get more info. doug On 01/25/2015 11:16 AM, angela.fav...@unipd.it wrote: Hi all, I wrote a paper about gyrification in a sample of malnourished patients. I found only little overlap between maps of significantly rediced cortical thickness and maps of significantly reduced gyrification index (in comparison to a group of healthy controls). One of the reviewer raised the question that this is not sufficient to demonstrate that reduced gyrification is not due to reduced cortical thickness (or GM volume) and suggest to perform a between group analysis using cortical thickness (or volume) maps as vertex-wise covariates. Is it possible to perform this type of analysis? I believe that QDEC does not allow it Thank you Angela Hi Maria it's really hard to say - you'll need to try it out. There aren't strong prior constraints on skull shape, but if the shape of the brain is too different, things may degrade Bruce On Fri, 23 Jan 2015, Maria Holland wrote: Hi all, I am starting a project analyzing patients with cranial deformities. How robust is the automatic cortical reconstruction process - i.e., would it be able to handle deformed skulls? Similar to this picture: http://upload.wikimedia.org/wikipedia/commons/1/1f/Single_suture_synostosis .png I am also wondering about the possibility of getting information about the intermediate steps of the local gyrification calculation. Like, could we get information on the pial and outer pial surface paths on each individual slice, before that information is turned into a 3D surface? Thanks for your help! ~ Maria ___ 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 ___ 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
[Freesurfer] longitudinal pipeline
Hi Freesurfer Experts, Is the longitudinal pipeline still recommended for the DTI data analysis if structural changes occur at different time points (e.g., pre and post-treatment)? Or is it better to use the standard pipeline? Are other options available? Thanks so much! Song ___ 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.
