Re: [Freesurfer] mri_segstats question
Hi Doug,
Thanks again for your help. I had two questions that came up from doing
some preliminary analysis with the mri_segstats:
1) When running the mri_segstats command with --seg
aparc+aseg_nocortex.mgz (which is the result of the matlab code you
provided below) and with --seg wmparc.mgz, even though the average
intensity is very close to each other, the individual intensities of same
structures are different. For instance
Left-Cerebral-White-Matter has an intensity of 145.3869 +/- 21.6883 with
--seg aparc+aseg_nocortex.mgz and an intensity of 149.6910 +/- 15.6547
with --aseg wmparc.mgz. Also the number of voxels of the same structure is
different in each case. Is there a reason why this is happening?
2) If I want to include the wm parcellation map to calculate the mean
intensity, I am assuming that wmparc.mgz would be the correct segmentation
volume to use, right?
3) If the answer to (2) is yes, and if I wanted to measure the average
intensity with --seg wmparc.mgz but after excluding the cortex, should I
run with --seg wmparc.mgz and just not take into consideration all the
*-ctx-* parcellations that come up in the stats file, or is there a way to
remove the cortex from wmparc.mgz and then run mri_segstats with the
wmparc_nocortex.mgz file as the --seg (I tried to subtract a binary map of
the cortex from wmparc.mgz, but had no luck: maybe I was doing something
wrong.)
Thanks in advance for your help!
Best,
Panos
>
> You can just do it in matlab, somethhing like
>
> a = MRIread('aparc+aseg.mgz');
> ind = find(a.vol > 999);
> a.vol(ind) = 0;
> MRIwrite(a,'nocortex.mgz')
>
>
>
> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> I'm sorry, what I meant to ask in the previous question is whether there
>> is a way to come up with a segmentation volume for the mri_segstats
>> command that is exactly like aseg.mgz but that does not include the
>> cortex. The reason I'm asking is because by using the aseg.mgz volume in
>> the --seg flag, you're also incorporating the intensity of the cortex
>> when
>> measuring the mean intensity of orig.mgz, but I wanted to see if there
>> was
>> a way to calculate the mean intensity of orig.mgz but without
>> incorporating the intensity of the cortex.
>>
>> Thanks again,
>> Panos
>>
>>> If you want the volume of cortex, you should definitely not use
>>> aseg.mgz. aparc+aseg is better, but the best is to use the
>>> surface-based
>>> measure found in aseg.stats
>>>
>>> doug
>>>
>>> On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks again for your reply. One last question: The aseg.mgz file
includes
the cortex as well. If I want to extract the cortex from the aseg.mgz
file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
subtract them, and then use the result in the mri_segstats command, or
is
there a different way?
Thanks,
Panos
> On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks for the quick reply! In addition:
>>
>> 1) The average intensity measure in the above example does not
>> include
>> the
>> intensity of the skull, just everything inside, right?
> It includes all the structures that are segmented in seg. If there is
> not a skull segmentation, then it will not be in the output list.
>> 2) Just to be clear on the purpose of including the segmentations in
>> the
>> command line: The segmentations only specify the areas of the brain
>> that
>> you would like to measure the intensity on, but besides that they
>> don't
>> provide any intensity info by themselves, would that be correct?
>> That
>> is
>> the purpose of the --i flag, right?
> Correct
> doug
>> Thanks again for your help,
>> Panos
>>
>>> On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi FS community,
I had some questions regarding the mri_segstats command:
1) In the excludeid flag, are the ids the ones shown in the
FreeSurferColorLUT.txt?
>>> Yes
2) In case I would like to measure the mean intensity of the orig
file
as
outlined in the second example in
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats:
mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg
--ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
--nonempty --excludeid 0 --sum bert.aseg.sum
--in $SUBJECTS_DIR/bert/mri/orig
is the --seg flag necessary in order to calculate only the mean
intensity
within the skull, or does it serve another purpose?
>>> The seg defines the segmentations (eg, 17 is hippocampus)
>>>
Thanks in advance,
Panos
___
Freesurfer mailing list
Freesurfe
Re: [Freesurfer] recon-all subject -qcache in a different version of freesurfer?
It is ok to run -qcache using 5.3. On 04/23/2014 10:54 PM, Yizhou Ma wrote: > Dear Freesurfer experts, > > I have processed my images and done analysis with cortical thickness > using FS510. Now that I want to do vertex-wise analysis with surface > area and volume, I learned that there is a bug in FS510 with this. > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.html) > Before I go on to use recon-all subject -qcache in FS530 to generate > vertex-wise surface area and volume maps, I want to make sure that > this would not cause concerns about use of mixed versions of > Freesurfer, or concerns about interpreting my cortical thickness and > surface area/volume findings together. And if it does, what should I do? > > Thanks a lot, > Cherry > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_segstats question
On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks again for your help. I had two questions that came up from doing
> some preliminary analysis with the mri_segstats:
>
> 1) When running the mri_segstats command with --seg
> aparc+aseg_nocortex.mgz (which is the result of the matlab code you
> provided below) and with --seg wmparc.mgz, even though the average
> intensity is very close to each other, the individual intensities of same
> structures are different. For instance
> Left-Cerebral-White-Matter has an intensity of 145.3869 +/- 21.6883 with
> --seg aparc+aseg_nocortex.mgz and an intensity of 149.6910 +/- 15.6547
> with --aseg wmparc.mgz. Also the number of voxels of the same structure is
> different in each case. Is there a reason why this is happening?
what are your command lines?
>
> 2) If I want to include the wm parcellation map to calculate the mean
> intensity, I am assuming that wmparc.mgz would be the correct segmentation
> volume to use, right?
mean intensity of what?
>
> 3) If the answer to (2) is yes, and if I wanted to measure the average
> intensity with --seg wmparc.mgz but after excluding the cortex, should I
> run with --seg wmparc.mgz and just not take into consideration all the
> *-ctx-* parcellations that come up in the stats file, or is there a way to
> remove the cortex from wmparc.mgz and then run mri_segstats with the
> wmparc_nocortex.mgz file as the --seg (I tried to subtract a binary map of
> the cortex from wmparc.mgz, but had no luck: maybe I was doing something
> wrong.)
>
> Thanks in advance for your help!
>
> Best,
> Panos
>
>
>
>
>> You can just do it in matlab, somethhing like
>>
>> a = MRIread('aparc+aseg.mgz');
>> ind = find(a.vol > 999);
>> a.vol(ind) = 0;
>> MRIwrite(a,'nocortex.mgz')
>>
>>
>>
>> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
>>> Hi Doug,
>>>
>>> I'm sorry, what I meant to ask in the previous question is whether there
>>> is a way to come up with a segmentation volume for the mri_segstats
>>> command that is exactly like aseg.mgz but that does not include the
>>> cortex. The reason I'm asking is because by using the aseg.mgz volume in
>>> the --seg flag, you're also incorporating the intensity of the cortex
>>> when
>>> measuring the mean intensity of orig.mgz, but I wanted to see if there
>>> was
>>> a way to calculate the mean intensity of orig.mgz but without
>>> incorporating the intensity of the cortex.
>>>
>>> Thanks again,
>>> Panos
>>>
If you want the volume of cortex, you should definitely not use
aseg.mgz. aparc+aseg is better, but the best is to use the
surface-based
measure found in aseg.stats
doug
On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi Doug,
>
> Thanks again for your reply. One last question: The aseg.mgz file
> includes
> the cortex as well. If I want to extract the cortex from the aseg.mgz
> file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and
> subtract them, and then use the result in the mri_segstats command, or
> is
> there a different way?
>
> Thanks,
> Panos
>
>> On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
>>> Hi Doug,
>>>
>>> Thanks for the quick reply! In addition:
>>>
>>> 1) The average intensity measure in the above example does not
>>> include
>>> the
>>> intensity of the skull, just everything inside, right?
>> It includes all the structures that are segmented in seg. If there is
>> not a skull segmentation, then it will not be in the output list.
>>> 2) Just to be clear on the purpose of including the segmentations in
>>> the
>>> command line: The segmentations only specify the areas of the brain
>>> that
>>> you would like to measure the intensity on, but besides that they
>>> don't
>>> provide any intensity info by themselves, would that be correct?
>>> That
>>> is
>>> the purpose of the --i flag, right?
>> Correct
>> doug
>>> Thanks again for your help,
>>> Panos
>>>
On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
> Hi FS community,
>
> I had some questions regarding the mri_segstats command:
>
> 1) In the excludeid flag, are the ids the ones shown in the
> FreeSurferColorLUT.txt?
Yes
> 2) In case I would like to measure the mean intensity of the orig
> file
> as
> outlined in the second example in
> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats:
>
> mri_segstats --seg $SUBJECTS_DIR/bert/mri/aseg
> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt
> --nonempty --excludeid 0 --sum bert.aseg.sum
> --in $SUBJECTS_DIR/bert/mri/orig
>
> is the --seg flag necessary in order to calculate only the mean
> intensity
> within
Re: [Freesurfer] Fwd: Fwd: V1 label
Hi all, I'm having a problem similar to Krista's, where I'm getting holes in a few labels (e.g. V1.label, MT.label, BA44.label, BA45.label) produced by the recon-all pipeline. Did you ever discover the solution to this issue? I'm running Freesurfer v5.3.0. Andrew On Thu, Oct 3, 2013 at 6:49 PM, Bruce Fischl wrote: > you can do it here: > > https://gate.nmr.mgh.harvard.edu/filedrop2/ > > On Thu, 3 Oct 2013, krista kelly wrote: > > Sure! Where/how do I upload the subject's folder? I've tried attaching a >> zipped copy to my email but it exceeds the size limit. >> Thanks! >> Krista >> >> >> On Thu, Oct 3, 2013 at 8:23 AM, Bruce Fischl >> wrote: >> Hi Krista >> >> I've never seen that happen before. Can you upload this subject >> and we will take a look? >> >> thanks >> Bruce >> On Wed, 2 Oct 2013, krista kelly wrote: >> >> >> Hi Bruce, >> I've tried twice to post this to the freesurfer mail >> list but it hasn't >> worked, I'm assuming because of the attached >> pictures. I'm going to try this >> again with only one picture and see if it works. >> >> I'm using the V1 labels that are automatically >> generated during recon-all (I >> think at autorecon step 28??). There are also V2 and >> MT labels that get >> generated. Are they the Hinds ones? I'm using >> freesurfer version 5.0 and >> have tried in 5.1 as well. >> >> Here are the commands I ran: >> >> recon-all -all -notal-check -cw256 -force -subjid >> BV20 -i >> ~/Desktop/New_CT_niis/BV20.nii.gz >> >> By holes, I mean that when I look at the label on >> the 3d brain in tksurfer, >> there are areas on the surface that are coloured in >> by the label. I've >> attached a photograph of the left hemisphere with >> the V1 label overlaid. >> It's even worse, and in both hemispheres, when I >> look at the cuneus label >> automatically generated with freesurfer. Is there >> something I'm doing wrong? >> Please let me know you're not able to see the >> snapshots. >> >> Thanks! >> Krista >> >> >> On Mon, Sep 23, 2013 at 5:10 PM, Bruce Fischl >> >> wrote: >> Hi Krista, >> >> which V1 label are you talking about? And when >> you say holes >> when you load it onto the 3D brain with >> tksurfer, what exactly >> do you mean? Can you send us a snapshot? >> Bruce >> >> >> On Mon, 23 Sep 2013, krista kelly wrote: >> >> Hi all, >> I'm having trouble with V1 labels that >> are mapped >> automatically in freesurfer. I've >> noticed that there >> are holes in the label when I load it >> onto a 3d >> brain in tksurfer. This happens more >> often for the >> left >> hemisphere and not so much for the >> right. I've found >> the problem persists even after doing >> manual edits >> of the borders and fixing the brain >> extraction. I >> was just wondering if anyone has had the >> same >> problem >> or knows how to fix it (see message >> previously >> posted below). >> >> Thanks! >> >> Hi Doug, >> >> Sorry it's been a while since I've ran >> the initial >> codes, but I think these are the labels >> automatically >> generated by Freesurfer v5.0 during >> recon-all >> (correct me if I'm wrong). Here's what I >> ran below: >> >> recon-all -all -notal-check -cw256 >> -force -subjid >> MB18 -i >> ~/Desktop/New_CT_niis/MB18.nii.gz >> >> then >> >> recon-all -force -s MB18 -qcache -i >> ~/Desktop/New_CT_niis/MB18.nii.gz >> >> I've checked a few more brains and >> noticed the same >> problem. I've also noticed that the left >> hemisphere >> is always worse than the right. When >> opening the >> brains in tkmedit, the labels are not
Re: [Freesurfer] recon-all subject -qcache in a different version of freesurfer?
Great. Thanks Doug. On Thu, Apr 24, 2014 at 10:39 AM, Douglas N Greve wrote: > > It is ok to run -qcache using 5.3. > > > On 04/23/2014 10:54 PM, Yizhou Ma wrote: > > Dear Freesurfer experts, > > > > I have processed my images and done analysis with cortical thickness > > using FS510. Now that I want to do vertex-wise analysis with surface > > area and volume, I learned that there is a bug in FS510 with this. > > ( > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-August/019903.html > ) > > Before I go on to use recon-all subject -qcache in FS530 to generate > > vertex-wise surface area and volume maps, I want to make sure that > > this would not cause concerns about use of mixed versions of > > Freesurfer, or concerns about interpreting my cortical thickness and > > surface area/volume findings together. And if it does, what should I do? > > > > Thanks a lot, > > Cherry > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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] gPPI Toolbox Version 13.1 for SPM has now been released
Version 13.1 of the gPPI toolbox (previously released versions were 7.12 and 13) is now available at http://www.nitrc.org/projects/gppi Version 13.1 now supports task-models from FSFAST and can read the model structure directly from your FSFAST analysis. Version 13.1 now support robust weighted least squares (rWLS) - requires your first level model to have been generated with the rWLS toolbox. The major changes are: (1) Integrated spm_spm and spm_spm_WB into the software, no patch is needed. P.wb=1 will use the whole brain approach. (2) Added ability to start with FSFAST first level models. (3) Added ability to do rWLS, if the rWLS was used in the first-level models. (4) Removed dependency of gzip on java. (5) A few other bells and whistles. (6) Added script to pre-extract VOI timeseries (7) Added the ability to use upsampled data or neural signal inputs Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_segstats question
>
> On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks again for your help. I had two questions that came up from doing
>> some preliminary analysis with the mri_segstats:
>>
>> 1) When running the mri_segstats command with --seg
>> aparc+aseg_nocortex.mgz (which is the result of the matlab code you
>> provided below) and with --seg wmparc.mgz, even though the average
>> intensity is very close to each other, the individual intensities of
>> same
>> structures are different. For instance
>> Left-Cerebral-White-Matter has an intensity of 145.3869 +/- 21.6883 with
>> --seg aparc+aseg_nocortex.mgz and an intensity of 149.6910 +/- 15.6547
>> with --aseg wmparc.mgz. Also the number of voxels of the same structure
>> is
>> different in each case. Is there a reason why this is happening?
> what are your command lines?
>>
The commands are:
mri_segstats --seg /mri/aparc+aseg_nocortex.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum
/stats/int.aparc+aseg_nocortex.sum --in
/mri/orig.mgz
and
mri_segstats --seg /mri/wmparc.mgz --ctab
$FREESURFER_HOME/FreeSurferColorLUT.txt --nonempty --excludeid 0 --sum
/stats/int.wmparc.sum --in /mri/orig.mgz
>> 2) If I want to include the wm parcellation map to calculate the mean
>> intensity, I am assuming that wmparc.mgz would be the correct
>> segmentation
>> volume to use, right?
> mean intensity of what?
>>
The mean intensity of orig.mgz.
>> 3) If the answer to (2) is yes, and if I wanted to measure the average
>> intensity with --seg wmparc.mgz but after excluding the cortex, should I
>> run with --seg wmparc.mgz and just not take into consideration all the
>> *-ctx-* parcellations that come up in the stats file, or is there a way
>> to
>> remove the cortex from wmparc.mgz and then run mri_segstats with the
>> wmparc_nocortex.mgz file as the --seg (I tried to subtract a binary map
>> of
>> the cortex from wmparc.mgz, but had no luck: maybe I was doing something
>> wrong.)
>>
>> Thanks in advance for your help!
>>
>> Best,
>> Panos
>>
>>
>>
>>
>>> You can just do it in matlab, somethhing like
>>>
>>> a = MRIread('aparc+aseg.mgz');
>>> ind = find(a.vol > 999);
>>> a.vol(ind) = 0;
>>> MRIwrite(a,'nocortex.mgz')
>>>
>>>
>>>
>>> On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
I'm sorry, what I meant to ask in the previous question is whether
there
is a way to come up with a segmentation volume for the mri_segstats
command that is exactly like aseg.mgz but that does not include the
cortex. The reason I'm asking is because by using the aseg.mgz volume
in
the --seg flag, you're also incorporating the intensity of the cortex
when
measuring the mean intensity of orig.mgz, but I wanted to see if there
was
a way to calculate the mean intensity of orig.mgz but without
incorporating the intensity of the cortex.
Thanks again,
Panos
> If you want the volume of cortex, you should definitely not use
> aseg.mgz. aparc+aseg is better, but the best is to use the
> surface-based
> measure found in aseg.stats
>
> doug
>
> On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi Doug,
>>
>> Thanks again for your reply. One last question: The aseg.mgz file
>> includes
>> the cortex as well. If I want to extract the cortex from the
>> aseg.mgz
>> file, should I binarize both the aseg.mgz and aparc_aseg.mgz files
>> and
>> subtract them, and then use the result in the mri_segstats command,
>> or
>> is
>> there a different way?
>>
>> Thanks,
>> Panos
>>
>>> On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote:
Hi Doug,
Thanks for the quick reply! In addition:
1) The average intensity measure in the above example does not
include
the
intensity of the skull, just everything inside, right?
>>> It includes all the structures that are segmented in seg. If there
>>> is
>>> not a skull segmentation, then it will not be in the output list.
2) Just to be clear on the purpose of including the segmentations
in
the
command line: The segmentations only specify the areas of the
brain
that
you would like to measure the intensity on, but besides that they
don't
provide any intensity info by themselves, would that be correct?
That
is
the purpose of the --i flag, right?
>>> Correct
>>> doug
Thanks again for your help,
Panos
> On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote:
>> Hi FS community,
>>
>> I had some questions regarding the mri_segstats command:
>>
>> 1) In the excludeid flag, are the ids the ones shown in the
>> FreeSurferColorLUT.txt?
>
Re: [Freesurfer] FS QA Tools: Output, html and .gif Files
Hello, I just wanted to follow up to note that I did a bit more digging, and compared the freesurfer log files on this new batch, versus that which was successfully run last August. There are no differences in terms of the log files, with the exception of course that additional people were run. I also completely re-ran everyone, and removed the old successfully run files to a back-up drive to be able to go from scratch, and have still not been able to generate the snapshots. ImageMagik and GNU awk are both up to date. Any suggestions? Thanks, Jessica On Mon, Apr 21, 2014 at 10:52 AM, Jessica Bernard wrote: > Hi All, > > I've been running the Freesurfer QA Tools on some new data, and have been > having some difficulties with the outputs. I am running this using the > -snaps-detailed flag. In the past, we have had .html links, but also > detailed .gif files for each person. We've consistently had trouble with > the .html links, but the .gif files have been perfectly fine. However, when > running new individuals, not only are the images broken in the .html > output, but there are no gif files (which are preferred). Is there an > additional command that needs to be added to generate the detailed gif > files as well? Sorry if this is a rather basic question. I recently took > over the Freesurfer QA process, and am relatively new to the functions, and > my predecessor does not know how they created the gif files (the first > batch of QA was run 6 months ago with our first wave of data collection). > Thanks in advance for any help you may be able to provide. > > Best Wishes, > Jessica > ___ 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] Hippocampal subfields on 1.5 Tesla
Hi Bruce and FreeSurfers: I have received a manuscript to review for possible publication. The authors have used the subfields algorithm on 1.5T scans and obtained a parcellation with values. They have drawn some major conclusions on the basis of the findings. My understanding is that this method can only be done on 3T. Is the 1.5T results valid? Please advice. thanks, Alan Francis ___ 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] Problem with Monte Carlo Simulation
Hi, I am having problem when running the Monte Carlo script. The script seems to fail after only a few simulations but it does not give me any error message, it just says 'killed'. I am running it on 126 participants (2 groups of 63) and I have tried it on a number of different measures (sulc, area etc.). I thought it may be an space issue but I cleared all other files but that did not seem to make any difference. This is what is printed out on the terminal: [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 --sim mc-z 1 1.3 mc-z.negative --sim-sign neg --overwritecmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 --surf fsaverage rh --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat --C /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat WARNING: unrecognized mri_glmfit cmd option dods SURFACE: fsaverage rh /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim--glmdir Rh_JacobianW_15 --sim mc-z 1 1.3 mc-z.negative --sim-sign neg --overwrite$Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $Thu Apr 24 18:58:31 IST 2014Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linuxfitzgejesetenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0DoPoll = 0DoPBSubmit = 0DoBackground = 0DiagCluster = 0gd2mtx = dodsfwhm = 21.770250nSimPerJob = 11/1 Thu Apr 24 18:58:31 IST 2014mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx --mask Rh_JacobianW_15/mask.mgh --sim mc-z 1 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh whiteINFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed reading group avg surface area 822 cm^2 from fileReading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mghreading group avg surface area 822 cm^2 from fileReading in average area /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mghsimbase Rh_JacobianW_15/csd/mc-z.negative.j001gdfReadHeader: reading Rh_JacobianW_15/y.fsgdINFO: demeaning continous variablesContinuous Variable Means (all subjects)Class Means of each Continuous Variable1 groupASD2 groupCTRLINFO: gd2mtx_method is dodsReading source surface /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.whiteNumber of vertices 163842Number of faces327680Total area 65020.765625AvgVtxArea 0.396850AvgVtxDist 0.717994StdVtxDist 0.193566INFO: fwhm2niters: NOT fixing group surface areaSurface smoothing by fwhm=21.770250, niters=441.00 $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $cwd /projects/pi-lgallagh/HPC_12_00408/qdeccmdline mri_glmfit --y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx --C Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx --mask Rh_JacobianW_15/mask.mgh --sim mc-z 1 1.3 Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 --fsgd Rh_JacobianW_15/y.fsgd dods --label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --surf fsaverage rh white sysname Linuxhostname lonsdale01.clustermachine x86_64user fitzgejeFixVertexAreaFlag = 1UseMaskWithSmoothing 1fwhm 21.770250niters441.00OneSampleGroupMean 0y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mghlogyflag 0usedti 0FSGD Rh_JacobianW_15/y.fsgdlabelmask /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.labelmask Rh_JacobianW_15/mask.mghmaskinv 0glmdir (null)IllCondOK 0DoFFx 0Loading y from /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mghINFO: gd2mtx_method is dodsMatrix condition is 1/projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.labelFound 149926 points in label.Found 149926 voxels in masksearch space = 75188.6DOF = 124thresh = 1.3, threshadj = 0.99897 Starting simulation sim over 1 trialsSmoothing done, nsteps = 441, tsec = 69.733Smoothing done, nsteps = 441, tsec = 69.799Smoothing done, nsteps = 441, tsec = 69.754Smoothing done, nsteps = 441, tsec = 69.749Smoothing done, nsteps = 441, tsec = 69.743Smoothing done, nsteps
Re: [Freesurfer] Problem with Monte Carlo Simulation
First of all, do you really need to run the simulation? If you are just doing a whole hemisphere analysis on fsaverage, then you can use the precomputed option. doug On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote: > Hi, > > I am having problem when running the Monte Carlo script. The script > seems to fail after only a few simulations but it does not give me any > error message, it just says 'killed'. I am running it on 126 > participants (2 groups of 63) and I have tried it on a number of > different measures (sulc, area etc.). I thought it may be an space > issue but I cleared all other files but that did not seem to make any > difference. > > This is what is printed out on the terminal: > > [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 > --sim mc-z 1 1.3 mc-z.negative --sim-sign neg --overwrite > > cmdline mri_glmfit --y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods > --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 > --surf fsaverage rh --label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat > > --C > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat > > > > > WARNING: unrecognized mri_glmfit cmd option dods > > > SURFACE: fsaverage rh > > /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim > > --glmdir Rh_JacobianW_15 --sim mc-z 1 1.3 mc-z.negative --sim-sign > neg --overwrite > > $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $ > > Thu Apr 24 18:58:31 IST 2014 > > Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 > 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > fitzgeje > > setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/ > > FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0 > > DoPoll = 0 > > DoPBSubmit = 0 > > DoBackground = 0 > > DiagCluster = 0 > > gd2mtx = dods > > fwhm = 21.770250 > > nSimPerJob = 1 > > 1/1 Thu Apr 24 18:58:31 IST 2014 > > mri_glmfit --y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > --C > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 1 1.3 > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 > --fsgd Rh_JacobianW_15/y.fsgd dods --label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > --surf fsaverage rh white > > INFO: ignoring tag Creator > > INFO: ignoring tag SUBJECTS_DIR > > INFO: ignoring tag SynthSeed > > reading group avg surface area 822 cm^2 from file > > Reading in average area > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > reading group avg surface area 822 cm^2 from file > > Reading in average area > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > simbase Rh_JacobianW_15/csd/mc-z.negative.j001 > > gdfReadHeader: reading Rh_JacobianW_15/y.fsgd > > INFO: demeaning continous variables > > Continuous Variable Means (all subjects) > > Class Means of each Continuous Variable > > 1 groupASD > > 2 groupCTRL > > INFO: gd2mtx_method is dods > > Reading source surface > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white > > Number of vertices 163842 > > Number of faces327680 > > Total area 65020.765625 > > AvgVtxArea 0.396850 > > AvgVtxDist 0.717994 > > StdVtxDist 0.193566 > > INFO: fwhm2niters: NOT fixing group surface area > > Surface smoothing by fwhm=21.770250, niters=441.00 > > > $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ > > cwd /projects/pi-lgallagh/HPC_12_00408/qdec > > cmdline mri_glmfit --y > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > --C > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 1 1.3 > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 > --fsgd Rh_JacobianW_15/y.fsgd dods --label > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > --surf fsaverage rh white > > sysname Linux > > hostname lonsdale01.cluster > > machine x86_64 > > user fitzgeje > > FixVertexAreaFlag = 1 > > UseMaskWithSmoothing 1 > > fwhm 21.770250 > > niters441.00 > > OneSampleGroupMean 0 > > y /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh > > logyflag 0 > > usedti 0 > > FSGD Rh_JacobianW_15/y.fsgd > > labelmask > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > mask Rh_JacobianW_15/mask.mgh > >
Re: [Freesurfer] mri_glmfit | constructing the "C.txt" and FSGD files
I responded to your email with the email. I did not respond to the 2nd question because you FSGD file was messed up and you never said what contrast you wanted to test. The contrast matrix must have number of columns equal to the number of regressors (6 in your case). In your case, if you wanted test for Patients vs Controls then your contrast is right On 04/23/2014 03:52 PM, Douglas N Greve wrote: > > Your coding for gender is probably wrong. The way you have it set up, > you are saying that gender#2 should have twice the thickness of gender > #1. You should set up 4 classes (PM, PF, CM, CF) > > > On 04/23/2014 03:40 PM, Baker, Justin T.,M.D.,Ph.D. wrote: >> Hi all, >> >> I'm trying to run what should be a very simple cortical thickness >> regression analysis in mri_glmfit, but could use some help with >> putting together my "C.txt" and FSGD files. >> I have two classes (e.g. Patient, Control) and two nuisance variables >> (i.e. Age, Gender). >> >> My FSGD file looks like this: >> GroupDescriptorFile 1 >> Title FS_Thickness >> Class Patient >> Class Control >> Variables Age Gender >> Input 130725_GB49NP Patient 18 1 >> Input 130620_HU64KP Patient 21 2 >> ... >> >> And my "C.txt" file looks like: >> 1 -1 0 0 0 0 >> ...which I'm pretty sure is wrong, but I don't quite understand what >> the columns mean, so any light shed would be appreciated! >> >> -Justin >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_glmfit | constructing the "C.txt" and FSGD files
Hi Freesurfer et al., Since no one has responded to my email below, I'll assume my question is poorly formed. I'm trying to compose an appropriate contrast matrix (what I've called the "C.txt" file) for a regression of surface thickness categorical comparison (two categories) with two nuisance variables. Can someone clarify what each column of the contrast file represents and how to set it up for this? I'm having trouble finding documentation of this. It is my hope that when I call: mri_glmfit --fsgd fsgd.txt --y lh.TEMP.mgh --C C.txt --surf fsaverage lh --cortex --glmdir lh.TEMP.output I am prepping to run a regression looking at the relationship between Patient status (i.e. 1 or 0) and cortical thickness, partialing out age and gender. Thanks in advance for any help you can offer, Justin On Apr 23, 2014, at 3:40 PM, Justin Baker wrote: > Hi all, > > I'm trying to run what should be a very simple cortical thickness regression > analysis in mri_glmfit, but could use some help with putting together my > "C.txt" and FSGD files. > I have two classes (e.g. Patient, Control) and two nuisance variables (i.e. > Age, Gender). > > My FSGD file looks like this: > GroupDescriptorFile 1 > Title FS_Thickness > Class Patient > Class Control > Variables Age Gender > Input 130725_GB49NP Patient 18 1 > Input 130620_HU64KP Patient 21 2 > ... > > And my "C.txt" file looks like: > 1 -1 0 0 0 0 > ...which I'm pretty sure is wrong, but I don't quite understand what the > columns mean, so any light shed would be appreciated! > > -Justin smime.p7s Description: S/MIME cryptographic signature ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Hippocampal subfields on 1.5 Tesla
Hi Alan, Typically subfields segmentation requires hi-resolution data (e.g. 0.4 x 0.4 mm in-plane resolution). The thickness of a CA subfield typically range between 0.5-1.00 mm, but 1.5 T data does not achieve sub-millimeter resolutions. Further, subfield segmentation typically requires high-contrast data to discern the internal boundaries formed by the stratum radiatum/stratum lacunosum-moleculare (SLRM). I doubt that images produced on a 1.5 T magnet can achieve the necessary contrast. Last, and please someone correct me if what I say is inaccurate, but doesn't the Van Leemput method use statistical priors to apply label probabilities in reference to a generated hippocampal surface? This would imply that the method assigns label probabilities without reference to a subject's SLRM intensity information. For volumetry, I am somewhat skeptical that a method that only relies on a generated surface would be sensitive to group x subfield interactions; especially double dissociations in which overall volume/shape of the hippocampus may be similar across groups. That the that was generated from potentially low resolution, low contrast data cannot help the matter. Some may disagree about this though and I'd be interested in hearing what other people think about the matter. In general, I am quite optimistic about automated methods to segment the subfields. Joshua - Joshua K. Lee Doctoral Candidate Department of Psychology & Center for Mind and Brain University of California, Davis On Thu, Apr 24, 2014 at 12:24 PM, Alan Francis wrote: > Hi Bruce and FreeSurfers: > > I have received a manuscript to review for possible publication. The > authors have used the subfields algorithm on 1.5T scans and obtained a > parcellation with values. They have drawn some major conclusions on the > basis of the findings. My understanding is that this method can only be > done on 3T. Is the 1.5T results valid? > > Please advice. > > thanks, > > Alan Francis > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Problem with Monte Carlo Simulation
Hi Doug, Thank you for your reply. By precomputed do you mean the FDR in the GUI? Apologies I'm still new to the program! I am planning on running an ROI analysis so will need to run it for that anyway (I think?) Best, Jackie On 24 April 2014 21:47, Douglas N Greve wrote: > > First of all, do you really need to run the simulation? If you are just > doing a whole hemisphere analysis on fsaverage, then you can use the > precomputed option. > > doug > > On 04/24/2014 02:20 PM, Jacqueline Elaine Fitzgerald wrote: > > Hi, > > > > I am having problem when running the Monte Carlo script. The script > > seems to fail after only a few simulations but it does not give me any > > error message, it just says 'killed'. I am running it on 126 > > participants (2 groups of 63) and I have tried it on a number of > > different measures (sulc, area etc.). I thought it may be an space > > issue but I cleared all other files but that did not seem to make any > > difference. > > > > This is what is printed out on the terminal: > > > > [fitzgeje@lonsdale01 qdec]$ mri_glmfit-sim --glmdir Rh_JacobianW_15 > > --sim mc-z 1 1.3 mc-z.negative --sim-sign neg --overwrite > > > > cmdline mri_glmfit --y > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --fsgd > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/qdec.fsgd dods > > --glmdir /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15 > > --surf fsaverage rh --label > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label --C > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Avg-Intercept-jacobian_white.mat > > --C > > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/contrasts/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mat > > > > > > > > WARNING: unrecognized mri_glmfit cmd option dods > > > > > > SURFACE: fsaverage rh > > > > /home/support/apps/apps/freesurfer/4.5.0/bin/mri_glmfit-sim > > > > --glmdir Rh_JacobianW_15 --sim mc-z 1 1.3 mc-z.negative --sim-sign > > neg --overwrite > > > > $Id: mri_glmfit-sim,v 1.1.2.20 2009/07/16 16:36:47 greve Exp $ > > > > Thu Apr 24 18:58:31 IST 2014 > > > > Linux lonsdale01.cluster 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 > > 11:13:47 CDT 2013 x86_64 x86_64 x86_64 GNU/Linux > > > > fitzgeje > > > > setenv SUBJECTS_DIR /projects/pi-lgallagh/HPC_12_00408/ > > > > FREESURFER_HOME /home/support/apps/apps/freesurfer/4.5.0 > > > > DoPoll = 0 > > > > DoPBSubmit = 0 > > > > DoBackground = 0 > > > > DiagCluster = 0 > > > > gd2mtx = dods > > > > fwhm = 21.770250 > > > > nSimPerJob = 1 > > > > 1/1 Thu Apr 24 18:58:31 IST 2014 > > > > mri_glmfit --y > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > > --C > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 1 1.3 > > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 > > --fsgd Rh_JacobianW_15/y.fsgd dods --label > > /projects/pi-lgallagh/HPC_12_00408/fsaverage/label/rh.cortex.label > > --surf fsaverage rh white > > > > INFO: ignoring tag Creator > > > > INFO: ignoring tag SUBJECTS_DIR > > > > INFO: ignoring tag SynthSeed > > > > reading group avg surface area 822 cm^2 from file > > > > Reading in average area > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > > > reading group avg surface area 822 cm^2 from file > > > > Reading in average area > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white.avg.area.mgh > > > > simbase Rh_JacobianW_15/csd/mc-z.negative.j001 > > > > gdfReadHeader: reading Rh_JacobianW_15/y.fsgd > > > > INFO: demeaning continous variables > > > > Continuous Variable Means (all subjects) > > > > Class Means of each Continuous Variable > > > > 1 groupASD > > > > 2 groupCTRL > > > > INFO: gd2mtx_method is dods > > > > Reading source surface > > /projects/pi-lgallagh/HPC_12_00408//fsaverage/surf/rh.white > > > > Number of vertices 163842 > > > > Number of faces327680 > > > > Total area 65020.765625 > > > > AvgVtxArea 0.396850 > > > > AvgVtxDist 0.717994 > > > > StdVtxDist 0.193566 > > > > INFO: fwhm2niters: NOT fixing group surface area > > > > Surface smoothing by fwhm=21.770250, niters=441.00 > > > > > > $Id: mri_glmfit.c,v 1.138.2.15 2009/07/27 17:43:10 greve Exp $ > > > > cwd /projects/pi-lgallagh/HPC_12_00408/qdec > > > > cmdline mri_glmfit --y > > /projects/pi-lgallagh/HPC_12_00408/qdec/Rh_JacobianW_15/y.mgh --C > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Avg-Intercept-jacobian_white.mtx > > --C > > > Rh_JacobianW_15/tmp.mri_glmfit-sim-21064/rh-Diff-ASD-CTRL-Intercept-jacobian_white.mtx > > --mask Rh_JacobianW_15/mask.mgh --sim mc-z 1 1.3 > > Rh_JacobianW_15/csd/mc-z.negative.j001 --sim-sign neg --fwhm 21.770250 > > --fsgd Rh_JacobianW_15/y.fsgd dods --label > > /projects/pi-lgallagh/HPC_12_0040
[Freesurfer] Regarding mri_path2label in computation of gyrification index
Hi, I am trying to compute gyrification index step by step for my dataset using the guidelines outlined on the website to compute lgi. I'm stuck at the step of mri_path2label command. What is the exact command to create a?h.pial.*.label file from?h.pial.*.path and?h.pial.*.center file? mri_path2label --(?) ?h.pial.*.path ?h.pial.*. center ?h.pial.*.label If I use --singlepath I could create *. label files but the results don't match the output created from recon_all -compute_lgi. Secondly, what is the meaning of the error MRIS‎alloc:nfaces=-8<0. Thank you for any help. Sincerely Virendra UT Southwestern Medical Center The future of medicine, today. ___ 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.
