Dear Freesurfer experts,
After a qdec contrast that asked where does thickness correlate with behavioural score, I got 2 significant clusters, and I would like, for each of these clusters, to have a list of extracted average thickness values (across the entire cluster), for each subject that I can then plot externally against the score values.
I tried applying answers to previous similar questions with no success; some of them suggested using mri_segstats, however I'm not very clear on how annotation files are to be used (I've only used the QDEC GUI), and I wasn't able to work out the syntax that would give me what I wanted (assuming mri_segstats is in fact the command to be used)
Thanks for any help!
Best wishes, Tudor
If you ran the clusterwise correction, then there will be an output file with the data you want already there. Run mri_glmfit-sim --help to get more info doug
On 03/31/2014 11:28 AM, Tudor Popescu wrote:
Dear Freesurfer experts,
After a qdec contrast that asked where does thickness correlate with behavioural score, I got 2 significant clusters, and I would like, for each of these clusters, to have a list of extracted average thickness values (across the entire cluster), for each subject that I can then plot externally against the score values.
I tried applying answers to previous similar questions with no success; some of them suggested using mri_segstats, however I'm not very clear on how annotation files are to be used (I've only used the QDEC GUI), and I wasn't able to work out the syntax that would give me what I wanted (assuming mri_segstats is in fact the command to be used)
Thanks for any help!
Best wishes, Tudor
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug, Presumably that file is mc-z.abs.th13.pdf.dat, which gets created after running the null-z correction. Based on the --help and on a previous threadhttps://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html, I gathered it's this command that I need: mri_glmfit-sim --glmdir mc-z.abs.th13.pdf.dat --cache 1.3 --sim-sign abs I ran it from the SUBJECTS_DIR folder, the design folder or the contrast folder (lh-Avg-pial_thickness-score-Cor), but in all cases it says "ERROR: cannot find mc-z.abs.th13.pdf.dat" Is this really the command I need to simply extract the values from the 2 clusters found in the analysis? THanks again Tudor
On 31 March 2014 17:44, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
If you ran the clusterwise correction, then there will be an output file with the data you want already there. Run mri_glmfit-sim --help to get more info doug
On 03/31/2014 11:28 AM, Tudor Popescu wrote:
Dear Freesurfer experts,
After a qdec contrast that asked where does thickness correlate with behavioural score, I got 2 significant clusters, and I would like, for each of these clusters, to have a list of extracted average thickness values (across the entire cluster), for each subject that I can then plot externally against the score values.
I tried applying answers to previous similar questions with no success; some of them suggested using mri_segstats, however I'm not very clear on how annotation files are to be used (I've only used the QDEC GUI), and I wasn't able to work out the syntax that would give me what I wanted (assuming mri_segstats is in fact the command to be used)
Thanks for any help!
Best wishes, Tudor
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 greve@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.
The file you are looking for should be something like mc-z.abs.th13.y.ocn.dat you dont need to run mri_glmfit-sim again
On 03/31/2014 12:25 PM, Tudor Popescu wrote:
Thanks Doug, Presumably that file is mc-z.abs.th13.pdf.dat, which gets created after running the null-z correction. Based on the --help and on a previous thread https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html, I gathered it's this command that I need: mri_glmfit-sim --glmdir mc-z.abs.th13.pdf.dat --cache 1.3 --sim-sign abs I ran it from the SUBJECTS_DIR folder, the design folder or the contrast folder (lh-Avg-pial_thickness-score-Cor), but in all cases it says "ERROR: cannot find mc-z.abs.th13.pdf.dat" Is this really the command I need to simply extract the values from the 2 clusters found in the analysis? THanks again Tudor
On 31 March 2014 17:44, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you ran the clusterwise correction, then there will be an output file with the data you want already there. Run mri_glmfit-sim --help to get more info doug On 03/31/2014 11:28 AM, Tudor Popescu wrote: > Dear Freesurfer experts, > > After a qdec contrast that asked where does thickness correlate with > behavioural score, I got 2 significant clusters, and I would like, for > each of these clusters, to have a list of extracted average thickness > values (across the entire cluster), for each subject that I can then > plot externally against the score values. > > I tried applying answers to previous similar questions with no > success; some of them suggested using mri_segstats, however I'm not > very clear on how annotation files are to be used (I've only used the > QDEC GUI), and I wasn't able to work out the syntax that would give me > what I wanted (assuming mri_segstats is in fact the command to be used) > > Thanks for any help! > > Best wishes, > Tudor > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug
The only OCN files I have in my qdec correlation contrast folder (after having run the MC-Z correction) are mc-z.abs.th13.sig.ocn.annot and mc-z.abs.th13.sig.ocn.mgh.
How should I obtain mc-z.abs.th13.y.ocn.dat, and what command (if not mri_glmfit-sim) should I use on it in order to extract values from the two clusters?
On 31 March 2014 18:35, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
The file you are looking for should be something like mc-z.abs.th13.y.ocn.dat you dont need to run mri_glmfit-sim again
On 03/31/2014 12:25 PM, Tudor Popescu wrote:
Thanks Doug, Presumably that file is mc-z.abs.th13.pdf.dat, which gets created after running the null-z correction. Based on the --help and on a previous thread <
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html
, I gathered it's this command that I need: mri_glmfit-sim --glmdir mc-z.abs.th13.pdf.dat --cache 1.3 --sim-sign abs I ran it from the SUBJECTS_DIR folder, the design folder or the contrast folder (lh-Avg-pial_thickness-score-Cor), but in all cases it says "ERROR: cannot find mc-z.abs.th13.pdf.dat" Is this really the command I need to simply extract the values from the 2 clusters found in the analysis? THanks again Tudor
On 31 March 2014 17:44, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
If you ran the clusterwise correction, then there will be an output file with the data you want already there. Run mri_glmfit-sim --help toget
more info doug On 03/31/2014 11:28 AM, Tudor Popescu wrote: > Dear Freesurfer experts, > > After a qdec contrast that asked where does thickness correlatewith
> behavioural score, I got 2 significant clusters, and I would like, for > each of these clusters, to have a list of extracted average thickness > values (across the entire cluster), for each subject that I canthen
> plot externally against the score values. > > I tried applying answers to previous similar questions with no > success; some of them suggested using mri_segstats, however I'm not > very clear on how annotation files are to be used (I've only used the > QDEC GUI), and I wasn't able to work out the syntax that would give me > what I wanted (assuming mri_segstats is in fact the command to be used) > > Thanks for any help! > > Best wishes, > Tudor > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
what version of FS are you running
On 03/31/2014 12:48 PM, Tudor Popescu wrote:
Hi Doug
The only OCN files I have in my qdec correlation contrast folder (after having run the MC-Z correction) are mc-z.abs.th13.sig.ocn.annot and mc-z.abs.th13.sig.ocn.mgh.
How should I obtain mc-z.abs.th13.y.ocn.dat, and what command (if not mri_glmfit-sim) should I use on it in order to extract values from the two clusters?
On 31 March 2014 18:35, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The file you are looking for should be something like mc-z.abs.th13.y.ocn.dat you dont need to run mri_glmfit-sim again On 03/31/2014 12:25 PM, Tudor Popescu wrote: > Thanks Doug, > Presumably that file is mc-z.abs.th13.pdf.dat, which gets created > after running the null-z correction. > Based on the --help and on a previous thread > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html>, > I gathered it's this command that I need: > mri_glmfit-sim --glmdir mc-z.abs.th13.pdf.dat --cache 1.3 > --sim-sign abs > I ran it from the SUBJECTS_DIR folder, the design folder or the > contrast folder (lh-Avg-pial_thickness-score-Cor), but in all cases it > says "ERROR: cannot find mc-z.abs.th13.pdf.dat" > Is this really the command I need to simply extract the values from > the 2 clusters found in the analysis? > THanks again > Tudor > > > On 31 March 2014 17:44, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > If you ran the clusterwise correction, then there will be an > output file > with the data you want already there. Run mri_glmfit-sim --help to get > more info > doug > > On 03/31/2014 11:28 AM, Tudor Popescu wrote: > > Dear Freesurfer experts, > > > > After a qdec contrast that asked where does thickness correlate with > > behavioural score, I got 2 significant clusters, and I would > like, for > > each of these clusters, to have a list of extracted average > thickness > > values (across the entire cluster), for each subject that I can then > > plot externally against the score values. > > > > I tried applying answers to previous similar questions with no > > success; some of them suggested using mri_segstats, however I'm not > > very clear on how annotation files are to be used (I've only > used the > > QDEC GUI), and I wasn't able to work out the syntax that would > give me > > what I wanted (assuming mri_segstats is in fact the command to > be used) > > > > Thanks for any help! > > > > Best wishes, > > Tudor > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
5.3.0
On 31 March 2014 19:07, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
what version of FS are you running
On 03/31/2014 12:48 PM, Tudor Popescu wrote:
Hi Doug
The only OCN files I have in my qdec correlation contrast folder (after having run the MC-Z correction) are mc-z.abs.th13.sig.ocn.annot and mc-z.abs.th13.sig.ocn.mgh.
How should I obtain mc-z.abs.th13.y.ocn.dat, and what command (if not mri_glmfit-sim) should I use on it in order to extract values from the two clusters?
On 31 March 2014 18:35, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
The file you are looking for should be something like mc-z.abs.th13.y.ocn.dat you dont need to run mri_glmfit-sim again On 03/31/2014 12:25 PM, Tudor Popescu wrote: > Thanks Doug, > Presumably that file is mc-z.abs.th13.pdf.dat, which gets created > after running the null-z correction. > Based on the --help and on a previous thread > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html
, > I gathered it's this command that I need: > mri_glmfit-sim --glmdir mc-z.abs.th13.pdf.dat --cache 1.3 > --sim-sign abs > I ran it from the SUBJECTS_DIR folder, the design folder or the > contrast folder (lh-Avg-pial_thickness-score-Cor), but in all cases it > says "ERROR: cannot find mc-z.abs.th13.pdf.dat" > Is this really the command I need to simply extract the values from > the 2 clusters found in the analysis? > THanks again > Tudor > > > On 31 March 2014 17:44, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > If you ran the clusterwise correction, then there will be an > output file > with the data you want already there. Run mri_glmfit-sim --help to get > more info > doug > > On 03/31/2014 11:28 AM, Tudor Popescu wrote: > > Dear Freesurfer experts, > > > > After a qdec contrast that asked where does thickness correlate with > > behavioural score, I got 2 significant clusters, and I would > like, for > > each of these clusters, to have a list of extracted average > thickness > > values (across the entire cluster), for each subject that I can then > > plot externally against the score values. > > > > I tried applying answers to previous similar questions with
no
> > success; some of them suggested using mri_segstats, however I'm not > > very clear on how annotation files are to be used (I've only > used the > > QDEC GUI), and I wasn't able to work out the syntax thatwould
> give me > > what I wanted (assuming mri_segstats is in fact the commandto
> be used) > > > > Thanks for any help! > > > > Best wishes, > > Tudor > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 greve@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
And did you run the clusterwise correction for multiple comparisons? Either from qdec or with mri_glmfit-sim? That y.ocn file should be there
On 03/31/2014 02:02 PM, Tudor Popescu wrote:
5.3.0
On 31 March 2014 19:07, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what version of FS are you running On 03/31/2014 12:48 PM, Tudor Popescu wrote: > Hi Doug > > The only OCN files I have in my qdec correlation contrast folder > (after having run the MC-Z correction) are mc-z.abs.th13.sig.ocn.annot > and mc-z.abs.th13.sig.ocn.mgh. > > How should I obtain mc-z.abs.th13.y.ocn.dat, and what command (if not > mri_glmfit-sim) should I use on it in order to extract values from the > two clusters? > > > > On 31 March 2014 18:35, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > The file you are looking for should be something like > mc-z.abs.th13.y.ocn.dat > you dont need to run mri_glmfit-sim again > > On 03/31/2014 12:25 PM, Tudor Popescu wrote: > > Thanks Doug, > > Presumably that file is mc-z.abs.th13.pdf.dat, which gets created > > after running the null-z correction. > > Based on the --help and on a previous thread > > > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html>, > > I gathered it's this command that I need: > > mri_glmfit-sim --glmdir mc-z.abs.th13.pdf.dat --cache 1.3 > > --sim-sign abs > > I ran it from the SUBJECTS_DIR folder, the design folder or the > > contrast folder (lh-Avg-pial_thickness-score-Cor), but in all > cases it > > says "ERROR: cannot find mc-z.abs.th13.pdf.dat" > > Is this really the command I need to simply extract the values from > > the 2 clusters found in the analysis? > > THanks again > > Tudor > > > > > > On 31 March 2014 17:44, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > If you ran the clusterwise correction, then there will be an > > output file > > with the data you want already there. Run mri_glmfit-sim > --help to get > > more info > > doug > > > > On 03/31/2014 11:28 AM, Tudor Popescu wrote: > > > Dear Freesurfer experts, > > > > > > After a qdec contrast that asked where does thickness > correlate with > > > behavioural score, I got 2 significant clusters, and I would > > like, for > > > each of these clusters, to have a list of extracted average > > thickness > > > values (across the entire cluster), for each subject that > I can then > > > plot externally against the score values. > > > > > > I tried applying answers to previous similar questions with no > > > success; some of them suggested using mri_segstats, > however I'm not > > > very clear on how annotation files are to be used (I've only > > used the > > > QDEC GUI), and I wasn't able to work out the syntax that would > > give me > > > what I wanted (assuming mri_segstats is in fact the command to > > be used) > > > > > > Thanks for any help! > > > > > > Best wishes, > > > Tudor > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Yes, in qdec I selected .05 for Monte-Carlo Null-Z and ran the correction, which created the mc-z.abs.th13.* files (but no y.ocn). I repeated the analysis just now - same result.
On 31 March 2014 20:13, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
And did you run the clusterwise correction for multiple comparisons? Either from qdec or with mri_glmfit-sim? That y.ocn file should be there
On 03/31/2014 02:02 PM, Tudor Popescu wrote:
5.3.0
On 31 March 2014 19:07, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what version of FS are you running On 03/31/2014 12:48 PM, Tudor Popescu wrote: > Hi Doug > > The only OCN files I have in my qdec correlation contrast folder > (after having run the MC-Z correction) are mc-z.abs.th13.sig.ocn.annot > and mc-z.abs.th13.sig.ocn.mgh. > > How should I obtain mc-z.abs.th13.y.ocn.dat, and what command (if not > mri_glmfit-sim) should I use on it in order to extract values from the > two clusters? > > > > On 31 March 2014 18:35, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > The file you are looking for should be something like > mc-z.abs.th13.y.ocn.dat > you dont need to run mri_glmfit-sim again > > On 03/31/2014 12:25 PM, Tudor Popescu wrote: > > Thanks Doug, > > Presumably that file is mc-z.abs.th13.pdf.dat, which gets created > > after running the null-z correction. > > Based on the --help and on a previous thread > > > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html
, > > I gathered it's this command that I need: > > mri_glmfit-sim --glmdir mc-z.abs.th13.pdf.dat --cache 1.3 > > --sim-sign abs > > I ran it from the SUBJECTS_DIR folder, the design folder or the > > contrast folder (lh-Avg-pial_thickness-score-Cor), but in all > cases it > > says "ERROR: cannot find mc-z.abs.th13.pdf.dat" > > Is this really the command I need to simply extract the values from > > the 2 clusters found in the analysis? > > THanks again > > Tudor > > > > > > On 31 March 2014 17:44, Douglas N Greve > <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu
> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > If you ran the clusterwise correction, then there will be an > > output file > > with the data you want already there. Run mri_glmfit-sim > --help to get > > more info > > doug > > > > On 03/31/2014 11:28 AM, Tudor Popescu wrote: > > > Dear Freesurfer experts, > > > > > > After a qdec contrast that asked where does thickness > correlate with > > > behavioural score, I got 2 significant clusters, and I would > > like, for > > > each of these clusters, to have a list of extracted average > > thickness > > > values (across the entire cluster), for each subject that > I can then > > > plot externally against the score values. > > > > > > I tried applying answers to previous similar questions with no > > > success; some of them suggested using mri_segstats, > however I'm not > > > very clear on how annotation files are to be used (I've only > > used the > > > QDEC GUI), and I wasn't able to work out the syntax that would > > give me > > > what I wanted (assuming mri_segstats is in fact the command to > > be used) > > > > > > Thanks for any help! > > > > > > Best wishes, > > > Tudor > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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/
> > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the > person to > > whom it is > > addressed. If you believe this e-mail was sent to you in > error and > > the e-mail > > contains patient information, please contact the Partners > > Compliance HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > > you in error > > but does not contain patient information, please contact the > > sender and properly > > dispose of the e-mail. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 greve@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
That is weird. the easiest thing is to just run mri_glmfit-sim using the same parameters as qdec is using. You can probably even get the command-line from the terminal window doug
On 03/31/2014 02:39 PM, Tudor Popescu wrote:
Yes, in qdec I selected .05 for Monte-Carlo Null-Z and ran the correction, which created the mc-z.abs.th13.* files (but no y.ocn). I repeated the analysis just now - same result.
On 31 March 2014 20:13, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
And did you run the clusterwise correction for multiple comparisons? Either from qdec or with mri_glmfit-sim? That y.ocn file should be there On 03/31/2014 02:02 PM, Tudor Popescu wrote: > 5.3.0 > > > On 31 March 2014 19:07, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > what version of FS are you running > > > On 03/31/2014 12:48 PM, Tudor Popescu wrote: > > Hi Doug > > > > The only OCN files I have in my qdec correlation contrast folder > > (after having run the MC-Z correction) are > mc-z.abs.th13.sig.ocn.annot > > and mc-z.abs.th13.sig.ocn.mgh. > > > > How should I obtain mc-z.abs.th13.y.ocn.dat, and what command > (if not > > mri_glmfit-sim) should I use on it in order to extract values > from the > > two clusters? > > > > > > > > On 31 March 2014 18:35, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > The file you are looking for should be something like > > mc-z.abs.th13.y.ocn.dat > > you dont need to run mri_glmfit-sim again > > > > On 03/31/2014 12:25 PM, Tudor Popescu wrote: > > > Thanks Doug, > > > Presumably that file is mc-z.abs.th13.pdf.dat, which gets > created > > > after running the null-z correction. > > > Based on the --help and on a previous thread > > > > > > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html>, > > > I gathered it's this command that I need: > > > mri_glmfit-sim --glmdir mc-z.abs.th13.pdf.dat > --cache 1.3 > > > --sim-sign abs > > > I ran it from the SUBJECTS_DIR folder, the design folder > or the > > > contrast folder (lh-Avg-pial_thickness-score-Cor), but in all > > cases it > > > says "ERROR: cannot find mc-z.abs.th13.pdf.dat" > > > Is this really the command I need to simply extract the > values from > > > the 2 clusters found in the analysis? > > > THanks again > > > Tudor > > > > > > > > > On 31 March 2014 17:44, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > > > > If you ran the clusterwise correction, then there will > be an > > > output file > > > with the data you want already there. Run mri_glmfit-sim > > --help to get > > > more info > > > doug > > > > > > On 03/31/2014 11:28 AM, Tudor Popescu wrote: > > > > Dear Freesurfer experts, > > > > > > > > After a qdec contrast that asked where does thickness > > correlate with > > > > behavioural score, I got 2 significant clusters, and > I would > > > like, for > > > > each of these clusters, to have a list of extracted > average > > > thickness > > > > values (across the entire cluster), for each subject > that > > I can then > > > > plot externally against the score values. > > > > > > > > I tried applying answers to previous similar > questions with no > > > > success; some of them suggested using mri_segstats, > > however I'm not > > > > very clear on how annotation files are to be used > (I've only > > > used the > > > > QDEC GUI), and I wasn't able to work out the syntax > that would > > > give me > > > > what I wanted (assuming mri_segstats is in fact the > command to > > > be used) > > > > > > > > Thanks for any help! > > > > > > > > Best wishes, > > > > Tudor > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the > > person to > > > whom it is > > > addressed. If you believe this e-mail was sent to you in > > error and > > > the e-mail > > > contains patient information, please contact the Partners > > > Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was > sent to > > > you in error > > > but does not contain patient information, please > contact the > > > sender and properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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
Looking in the command window, qdec seems to only produce mri_glmfit (but not mri_glmfit-sim) commands, which is probably why the file you mention is not being produced in my case
On 31 March 2014 20:55, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
That is weird. the easiest thing is to just run mri_glmfit-sim using the same parameters as qdec is using. You can probably even get the command-line from the terminal window doug
On 03/31/2014 02:39 PM, Tudor Popescu wrote:
Yes, in qdec I selected .05 for Monte-Carlo Null-Z and ran the correction, which created the mc-z.abs.th13.* files (but no y.ocn). I repeated the analysis just now - same result.
On 31 March 2014 20:13, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
And did you run the clusterwise correction for multiple comparisons? Either from qdec or with mri_glmfit-sim? That y.ocn file should be there On 03/31/2014 02:02 PM, Tudor Popescu wrote: > 5.3.0 > > > On 31 March 2014 19:07, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > what version of FS are you running > > > On 03/31/2014 12:48 PM, Tudor Popescu wrote: > > Hi Doug > > > > The only OCN files I have in my qdec correlation contrast folder > > (after having run the MC-Z correction) are > mc-z.abs.th13.sig.ocn.annot > > and mc-z.abs.th13.sig.ocn.mgh. > > > > How should I obtain mc-z.abs.th13.y.ocn.dat, and what command > (if not > > mri_glmfit-sim) should I use on it in order to extract values > from the > > two clusters? > > > > > > > > On 31 March 2014 18:35, Douglas N Greve > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > > > > > The file you are looking for should be something like > > mc-z.abs.th13.y.ocn.dat > > you dont need to run mri_glmfit-sim again > > > > On 03/31/2014 12:25 PM, Tudor Popescu wrote: > > > Thanks Doug, > > > Presumably that file is mc-z.abs.th13.pdf.dat, which gets > created > > > after running the null-z correction. > > > Based on the --help and on a previous thread > > > > > > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg34602.html
, > > > I gathered it's this command that I need: > > > mri_glmfit-sim --glmdir mc-z.abs.th13.pdf.dat > --cache 1.3 > > > --sim-sign abs > > > I ran it from the SUBJECTS_DIR folder, the design
folder
> or the > > > contrast folder (lh-Avg-pial_thickness-score-Cor), but in all > > cases it > > > says "ERROR: cannot find mc-z.abs.th13.pdf.dat" > > > Is this really the command I need to simply extract the > values from > > > the 2 clusters found in the analysis? > > > THanks again > > > Tudor > > > > > > > > > On 31 March 2014 17:44, Douglas N Greve > > <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > > > > > > > > If you ran the clusterwise correction, then there will > be an > > > output file > > > with the data you want already there. Run mri_glmfit-sim > > --help to get > > > more info > > > doug > > > > > > On 03/31/2014 11:28 AM, Tudor Popescu wrote: > > > > Dear Freesurfer experts, > > > > > > > > After a qdec contrast that asked where does thickness > > correlate with > > > > behavioural score, I got 2 significant clusters, and > I would > > > like, for > > > > each of these clusters, to have a list of extracted > average > > > thickness > > > > values (across the entire cluster), for each subject > that > > I can then > > > > plot externally against the score values. > > > > > > > > I tried applying answers to previous similar > questions with no > > > > success; some of them suggested using mri_segstats, > > however I'm not > > > > very clear on how annotation files are to be used > (I've only > > > used the > > > > QDEC GUI), and I wasn't able to work out the syntax > that would > > > give me > > > > what I wanted (assuming mri_segstats is in fact the > command to > > > be used) > > > > > > > > Thanks for any help! > > > > > > > > Best wishes, > > > > Tudor > > > > > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > > > Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> > > > Phone Number: 617-724-2358 > > > Fax: 617-726-7422 > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop:https://gate.nmr.mgh.harvard.edu/filedrop2
> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://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/ > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the > > person to > > > whom it is > > > addressed. If you believe this e-mail was sent to you in > > error and > > > the e-mail > > > contains patient information, please contact the Partners > > > Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was > sent to > > > you in error > > > but does not contain patient information, please > contact the > > > sender and properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://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/
> > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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 greve@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@nmr.mgh.harvard.edu
-
Douglas N Greve -
Tudor Popescu