If there is no effect in A vs C, then adding it in the Ftest will make it weaker than the t-test.
On 02/06/2017 11:54 AM, Leon Ernst wrote:
Dear Freesurfer experts,
I am comparing cortical thickness data of two patient groups (Group A; Group B) and one control group (Group C) without any covariates.
In a simple t-test I observe a significant difference in cortical thickness only between Group B and Group C in several clusters (corrected p!).
Now I am running an ANOVA ("Three Groups (One Factor/Three Levels), No Covariates") as documented in your FSGD examples.
In the output of the f-test (using the following matrix [1 -1 0; 1 0 -1]) the clusters from my t-test remain but do not survive the correction using "mri_glmfit sim" as below.
Do I have to correct the results of my f-test using mri_glmfit-sim? If yes, why do I reveal a significant group-difference in the corrected t-test and not in the corrected f-test?
mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces
Thank you very much in advance!
Sincerely,
Leon
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
thanks. What kind of format is it? How do I open it?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You don't need to open it. Just download it and put it in your path. You may want to call it something slightly differnt so that you don't confuse it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
thanks. What kind of format is it? How do I open it?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm so sorry, I don't know anything about programming... I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug and tried to run the whole thing again like this:
mris_anatomical_stats-doug -mgz -cortex $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
but then I got this error:
bash: mris_anatomical_stats-doug: command not found
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:08:26 Betreff: Re: [Freesurfer] extract area.pial stats
You don't need to open it. Just download it and put it in your path. You may want to call it something slightly differnt so that you don't confuse it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
thanks. What kind of format is it? How do I open it?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
try typing:
rehash
then run it again On Wed, 8 Feb 2017, Clara Kühn wrote:
I'm so sorry, I don't know anything about programming... I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug and tried to run the whole thing again like this:
mris_anatomical_stats-doug -mgz -cortex $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
but then I got this error:
bash: mris_anatomical_stats-doug: command not found
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:08:26 Betreff: Re: [Freesurfer] extract area.pial stats
You don't need to open it. Just download it and put it in your path. You may want to call it something slightly differnt so that you don't confuse it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
thanks. What kind of format is it? How do I open it?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It either has to be in your path or you need to supply the full path when running it, like this $SUBJECTS_DIR/mris_anatomical_stats-doug
On 02/08/2017 11:27 AM, Clara Kühn wrote:
I'm so sorry, I don't know anything about programming... I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug and tried to run the whole thing again like this:
mris_anatomical_stats-doug -mgz -cortex $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
but then I got this error:
bash: mris_anatomical_stats-doug: command not found
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:08:26 Betreff: Re: [Freesurfer] extract area.pial stats
You don't need to open it. Just download it and put it in your path. You may want to call it something slightly differnt so that you don't confuse it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
thanks. What kind of format is it? How do I open it?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you, I think it worked. I've attached the file again. There was one error message in the terminal output though:
atlas_icv (eTIV) = 1287829 mm^3 (det: 1.512705 ) /nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't exist, using old naming conventions
Is that something to worry about?
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:34:06 Betreff: Re: [Freesurfer] extract area.pial stats
It either has to be in your path or you need to supply the full path when running it, like this $SUBJECTS_DIR/mris_anatomical_stats-doug
On 02/08/2017 11:27 AM, Clara Kühn wrote:
I'm so sorry, I don't know anything about programming... I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug and tried to run the whole thing again like this:
mris_anatomical_stats-doug -mgz -cortex $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
but then I got this error:
bash: mris_anatomical_stats-doug: command not found
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:08:26 Betreff: Re: [Freesurfer] extract area.pial stats
You don't need to open it. Just download it and put it in your path. You may want to call it something slightly differnt so that you don't confuse it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
thanks. What kind of format is it? How do I open it?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
No. The program is from version 6 so it is expecting v6 naming conventions
On 02/08/2017 11:38 AM, Clara Kühn wrote:
Thank you, I think it worked. I've attached the file again. There was one error message in the terminal output though:
atlas_icv (eTIV) = 1287829 mm^3 (det: 1.512705 ) /nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't exist, using old naming conventions
Is that something to worry about?
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:34:06 Betreff: Re: [Freesurfer] extract area.pial stats
It either has to be in your path or you need to supply the full path when running it, like this $SUBJECTS_DIR/mris_anatomical_stats-doug
On 02/08/2017 11:27 AM, Clara Kühn wrote:
I'm so sorry, I don't know anything about programming... I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug and tried to run the whole thing again like this:
mris_anatomical_stats-doug -mgz -cortex $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
but then I got this error:
bash: mris_anatomical_stats-doug: command not found
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:08:26 Betreff: Re: [Freesurfer] extract area.pial stats
You don't need to open it. Just download it and put it in your path. You may want to call it something slightly differnt so that you don't confuse it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
thanks. What kind of format is it? How do I open it?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
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
alright. Thank you so much!
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:45:38 Betreff: Re: [Freesurfer] extract area.pial stats
No. The program is from version 6 so it is expecting v6 naming conventions
On 02/08/2017 11:38 AM, Clara Kühn wrote:
Thank you, I think it worked. I've attached the file again. There was one error message in the terminal output though:
atlas_icv (eTIV) = 1287829 mm^3 (det: 1.512705 ) /nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't exist, using old naming conventions
Is that something to worry about?
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:34:06 Betreff: Re: [Freesurfer] extract area.pial stats
It either has to be in your path or you need to supply the full path when running it, like this $SUBJECTS_DIR/mris_anatomical_stats-doug
On 02/08/2017 11:27 AM, Clara Kühn wrote:
I'm so sorry, I don't know anything about programming... I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug and tried to run the whole thing again like this:
mris_anatomical_stats-doug -mgz -cortex $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
but then I got this error:
bash: mris_anatomical_stats-doug: command not found
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 17:08:26 Betreff: Re: [Freesurfer] extract area.pial stats
You don't need to open it. Just download it and put it in your path. You may want to call it something slightly differnt so that you don't confuse it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
thanks. What kind of format is it? How do I open it?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas N Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 16:43:47 Betreff: Re: [Freesurfer] extract area.pial stats
Try this version (same as version 6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
Hi Doug,
thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file for you to take a look at. As far as I can tell it's still reporting the white surface area. Or am I reading it wrong?
Cheers Clara
----- Ursprüngliche Mail ----- Von: "Douglas Greve" greve@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Mittwoch, 8. Februar 2017 00:15:22 Betreff: Re: [Freesurfer] extract area.pial stats
try
cd $SUBJECTS_DIR/subject/surf
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White Surface Area in the ?h.aparc.stats file. I have tried this command but it doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
How could I extract the total Pial Surface Area for each participant?
Thank you for you help! Clara _______________________________________________ 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.
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@nmr.mgh.harvard.edu
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Bruce Fischl -
Clara Kühn -
Douglas Greve -
Douglas N Greve
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Leon Ernst