Re: [Freesurfer] recon-all bug
External Email - Use Caution Hi freesurfer team, I've tried running recon-all as mentioned before with the -xf flag under different conditions. As far as I can tell, any line using the UpdateNeeded function. e.g.: "set ud = `UpdateNeeded $thickness $pial $white`" fails with the following if statement because the variable $ud includes paths as strings in it instead of a 0/1 integer. Setting it to a 1 or 0 beforehand also seems to solve the problem. The function UpdateNeeded only seems to return an integer as an exit status, so I'm not sure why there are path strings in it causing it to fail. If I print out the $ud variable before it fails and the result is: "/subjectDirectory/subjectID_FREESURFER/mri mri mri_FREESURFER /subjectDirectory/subjectID_FREESURFER/mri/mri_FREESURFER/stats 1" It returns the exit status of 1 preceded by the path of the subject's mri directory, just "mri", "mri_FREESURFER" and the subject's stats directory (all subjects in this particular study have the suffix "_FREESURFER"). It prints this out these strings no matter the variables as .mgz file names, or number of variables passed to the UpdateNeeded function. I still don't have a clue what would cause this behavior. The UpdateNeeded function seems to work fine and as intended as far as I can tell, so I still don't know why these paths/strings are being added and causing it to crash. Best, Kody Zalewski Message: 3 Date: Fri, 02 Apr 2021 03:49:02 +0200 From: fsbuild Subject: Re: [Freesurfer] recon-all bug To: freesurfer@nmr.mgh.harvard.edu Cc: cm...@neurosurgery.washington.edu Message-ID: <1617328142.6066780ef2...@trashmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hello Kody, One thing you could try to get more information printed about what is going on is to edit the very first line in the recon-all script to be: #! /bin/tcsh -xf ? instead of #! /bin/tcsh -f Adding the x option will echo each line in the script as it?s run with the variable values expanded, and seeing that output could help with debugging. - R. On Apr 1, 2021, at 20:29, zalewk zal...@uw.edu wrote:External Email - Use CautionHi Freesurfer team,My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all..I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine. Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem.It seems the $ud variable is for checking if updates are ! needed fo r a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient.Best,Kody Zalewski___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] recon-all bug
External Email - Use Caution Hi Freesurfer team, My lab recently switched over from FS6 to FS7 and I think I've encountered a bug with recon-all. I'm running subjects stepwise and editing them, running recon-all with the -autorecon2 and -autorecon3 flags initially are no problem, they run fine. Trying to re-run them or use the -autorecon2-wm, -autorecon-pial etc. flags lead to crashing at certain parts of the program. The error message I get is "if: expression syntax". Digging into the code, it seems to crash when it hits a line of code "if($ud || $ForceUpdate)". The syntax superficially looks right (I don't know tcsh), checking the variables it seems like $ForceUpdate is never set, but removing it from recon-all doesn't fix the problem. It seems the $ud variable is for checking if updates are needed for a set of volumes passed to the program. I don't know why that would be a problematic argument, removing that part seems to fix it, but this also seems like an important variable and I don't know enough about tcsh to understand why it works after removing it. Can one of the folks who wrote the recon-all script help me out? I'm running the commands step-wise as a work-around, but that is much less convenient. Best, Kody Zalewski ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks for getting back to me Doug/Bruce.
Sounds good, yes I definitely would want to wait until the bugs have been w=
orked out before utilizing latest release.
If your dev team needs contributors to document/write the ex-vivo processin=
g stream I'd be happy to step in and help, I've been running various ex-viv=
o scan acquisitions through freesurfer for a year at this point. I also hav=
e experience in C and shell scripting if that helps, as it seems that's wha=
t much of freesurfer is written in.
Not sure who I would talk to about that.
Best,
Kody Zalewski
Message: 11
Date: Tue, 19 Mar 2019 14:53:30 +
From: "Greve, Douglas N.,Ph.D."
Subject: Re: [Freesurfer] Omitting aseg regions from segmentationTo: "frees=
ur...@nmr.mgh.harvard.edu"
Message-ID: <235d9f13-1eda-1d76-920f-d30b9c467...@mgh.harvard.edu>
Content-Type: text/plain; charset=3D"windows-1252"
... but know that the dev version is not fully tested -- there may be signi=
ficant bugs that will not be uncovered until it is tested. As such, we may =
not be able to support any problems you run into.
On 3/18/19 8:12 PM, Bruce Fischl wrote:
Hi Kody
there definitely are flags like this in the dev version. e.g.:
case "-no-cerebellum":
case "-nocerebellum":
case "-NO-CEREBELLUM":
case "-NOCEREBELLUM":
set nocerebellum=3D( -nocerebellum)
breaksw ;
Maybe you should just grab the dev version?
And sorry, we haven't documented the ex vivo processing stream yet as it is=
too much of a work-in-progress.
cheers
Bruce
On Thu, 14 Mar 2019, zalewk wrote:
External Email - Use Caution
Hi Bruce,
In response to your previous email, in v6.0 it doesn't look like recon-all =
has a "-no-cerebellum"
flag (or any cerebellum-related flags), I did verify that the recon-all scr=
ipt in the bin folder had
hemisphere-specific flags available however.
Is there any documentation on this? It still seems as if I'm missing someth=
ing here, was it maybe
included in previous versions of freesurfer and removed?
Best,
Kody Zalewski
Date: Mon, 4 Mar 2019 15:07:26 -0500 (EST)
From: Bruce Fischl <mailto:fis...@nmr.mgh.harva=
rd.edu>
Subject: Re: [Freesurfer] Omitting aseg regions from segmentation
To: Freesurfer support list <mailto:freesur=
f...@nmr.mgh.harvard.edu>
Message-ID:
Content-Type: text/plain; charset=3D"iso-8859-1"
Hi Kody
yes, there are some hidden options to recon-all for this. Take a look at
the script for things like -no-cerebellum, -rh-only, and see if they are
sufficient for what you are trying to do
cheers
Bruce
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Use Caution<=
/p>
Thanks for getting back to me Doug/Bruce.
Sounds good, yes I definitely would want to wait until the bugs have been w=
orked out before utilizing latest release.
If your dev team needs contributors to document/write the ex-vivo processin=
g stream I'd be happy to step in and help, I've been running various ex-viv=
o scan acquisitions through freesurfer for a year at this point. I also hav=
e experience in C and shell scripting
if that helps, as it seems that's what much of freesurfer is written in. <=
br>
Not sure who I would talk to about that.
Best,
Kody Zalewski
Message: 11
Date: Tue, 19 Mar 2019 14:53:30
From: Greve, Douglas N.,Ph.D. dgr...@mgh.harvard.edu
Subject: Re: [Freesurfer] Omitting aseg regions from segmentationTo: =
freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu=
Message-ID: 235d9f13-1eda-1d76-920f-d30b9c467...@mgh.harvard.edu
Content-Type: text/plain; charset=3Dwindows-1252
... but know that the dev version is not fully tested -- there may be signi=
ficant bugs that will not be uncovered until it is tested. As such, we may =
not be able to support any problems you run into.
On 3/18/19 8:12 PM, Br=
uce Fischl wrote:
Hi Kody
there definitely are flags like this in the dev version. e.g.:
case -no-cerebellum:
case -nocerebel
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Subject: [Freesurfer] Omitting aseg regions from segmentation
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Hi Bruce,
In response to your previous email, in v6.0 it doesn't look like recon-all =
has a "-no-cerebellum" flag (or any cerebellum-related flags), I did verify=
that the recon-all script in the bin folder had hemisphere-specific flags =
available however.
Is there any documentation on this? It still seems as if I'm missing someth=
ing here, was it maybe included in previous versions of freesurfer and remo=
ved?
Best,
Kody Zalewski
Date: Mon, 4 Mar 2019 15:07:26 -0500 (EST)
From: Bruce Fischl
Subject: Re: [Freesurfer] Omitting aseg regions from segmentation
To: Freesurfer support list
Message-ID:
Content-Type: text/plain; charset=3D"iso-8859-1"
Hi Kody
yes, there are some hidden options to recon-all for this. Take a look at
the script for things like -no-cerebellum, -rh-only, and see if they are
sufficient for what you are trying to do
cheers
Bruce
On Mon, 4 Mar 2019, zalewk wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer team,
>
> I am currently working processing the volumetrics of exvivo brains, many =
of which do not have a
> brainstem/cerebellum.
> It seems this often results in a subcortical alignment that isn't optimal=
, and fails to create the
> pial/wm surface where freesurfer attempts to label more ventral non-zero =
voxels as
> brainstem/cerebellum. Currently, I have to manually edit the aseg.auto_no=
CCseg.label_intensities.mgz
> and aseg.presurf.mgz to fix this.
>
> Is there a way to omit aseg labels (like the brainstem/cerebellum) from t=
he processing stream that
> I've overlooked? If not, would there be a potential alternate solution su=
ch as creating a second
> atlas from the original sans these ROIs and have the cross-sectional stre=
am still run normally?
>
> Best,
> Kody Zalewski
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Hello Freesurfer Team,
Sorry to bother you guys again, any word on what you think is the best appr=
oach going forward here?
Best,
Kody Zalewski
From: zalewk
Sent: Thursday, June 7, 2018 10:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Longitudinal analysis of multiple scanner acquisitions
Good afternoon Freesurfer team,
I want to run the longitudinal pipeline on multiple groups of subjects, the=
problem is we are at the mercy of the scanners available to us at the vari=
ous time-points. We have two different Siemens 1.5 scanners (same type of s=
canner, there was an effort made to match them) at time point 1 and 2 with =
a Phillips 3T at time point 3. Is it worth the time to attempt a longitudin=
al analysis on this cohort?
Best,
Kody Zalewski
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/p>
Hello Freesurfer Team,
Sorry to bother you guys again, any word on what you think is the best appr=
oach going forward here?
Best,
Kody Zalewski
From: zalewk
Sent: Thursday, June 7, 2018 10:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Longitudinal analysis of multiple scanner acquisitions
Good afternoon Freesurfer team,<=
br>
I want to run the longitudinal pipeline on multiple groups of subjects, the=
problem is we are at the mercy of the scanners available to us at the vari=
ous time-points. We have two different Siemens 1.5 scanners (same type of s=
canner, there was an effort made
to match them) at time point 1 and 2 with a Phillips 3T at time point 3. I=
s it worth the time to attempt a longitudinal analysis on this cohort?
Best,
Kody Zalewski
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[Freesurfer] Longitudinal analysis of multiple scanner acquisitions
External Email - Use Caution Good afternoon Freesurfer team, I want to run the longitudinal pipeline on multiple groups of subjects, the problem is we are at the mercy of the scanners available to us at the various time-points. We have two different Siemens 1.5 scanners (same type of scanner, there was an effort made to match them) at time point 1 and 2 with a Phillips 3T at time point 3. Is it worth the time to attempt a longitudinal analysis on this cohort? Best, Kody Zalewski ___ 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] clarification
My apologies as I misstated some of the data in my first email, The voxel sizes are relatively similar, (two of the acquisitions are 1mm vs one with 0.9mm). Whereas the FOV is different between the scans being 256x256x176 on one acquisition, 224x256x176 on the second and 240x240x180 on the third. KZ On Tue, 5 Jul 2016, zal...@u.washington.edu wrote: > Hello Freesurfer team, > > I have the unfortunate task of performing longitudinal volumetric analysis on > subjects collected on three different scanners with different voxel > numbers/sizes. I didn't find this out until attempting to run the > longitudinal base and receiving this message: > > WARNING: Image geometries differ across time, maybe due to aquisition changes? > This can potentially bias a longitudinal study! Will continue in 10s. > > By re-registering the original nifti and recreating the norm.mgz/talairach I > can correct the geometry, but FSL's Flirt will only work with niftis and not > mgz volumes, ergo I can't re-register the manually edited brainmask/wm > volumes properly. > I was wondering if there were any freesurfer tools I could use to simply > re-register the .mgz volumes to the new norm.mgz? If so, how would I go about > doing that? Seeing as the brainmask/wm are both registered to 256^3/1mm > anyhow, is this something I should even be concerned about? > > Thanks, > KZ > > > ___ 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] Registering scans with different voxel sizes/numbers
Hello Freesurfer team, I have the unfortunate task of performing longitudinal volumetric analysis on subjects collected on three different scanners with different voxel numbers/sizes. I didn't find this out until attempting to run the longitudinal base and receiving this message: WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. By re-registering the original nifti and recreating the norm.mgz/talairach I can correct the geometry, but FSL's Flirt will only work with niftis and not mgz volumes, ergo I can't re-register the manually edited brainmask/wm volumes properly. I was wondering if there were any freesurfer tools I could use to simply re-register the .mgz volumes to the new norm.mgz? If so, how would I go about doing that? Seeing as the brainmask/wm are both registered to 256^3/1mm anyhow, is this something I should even be concerned about? Thanks, KZ ___ 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] QA measures mgz
Excellent, thank you for sharing! I have one more question. When running the mri_cnr function I tried using a number of different .mgz files with varying results, which would you recommend for the most accurate gm/wm and gm/csf CNR? Best, KZ -- Message: 1 Date: Fri, 17 Jul 2015 18:24:28 +0200 From: Jacek Manko j...@wp.pl Subject: Re: [Freesurfer] QA measures To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: 55a92c3ce71501.52368...@wp.pl Content-Type: text/plain; charset=iso-8859-2 You may find this paper useful: http://www.biomedcentral.com/1471-2342/12/27 Authors describe there some measures such as Euler number and #8220;Contrast to Noise ratio (CNR). Actually, they dont belong to QA package, but they are definitely worth looking at. Best, Jacek Manko Dnia 17-07-2015 o godz. 0:03 zal...@u.washington.edu napisa?(a): Dear Freesurfer Team, We would like to have a Q/A measure (or two) that would give us indication of how well your software worked on each of our data sets. Obviously some image sets will be noisier than others for a variety of reasons. Could you point us towards what options we may have for extracting such a measure from your processing pipeline? We were playing around with QAtools but wanted to understand if there is a systematic computation of say a handful of variables that would give us a global representation of how well things worked for each case we run? Something that we could compare across our patients and even across data sets? Best, KZ ___ 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] QA measures
Dear Freesurfer Team, We would like to have a Q/A measure (or two) that would give us indication of how well your software worked on each of our data sets. Obviously some image sets will be noisier than others for a variety of reasons. Could you point us towards what options we may have for extracting such a measure from your processing pipeline? We were playing around with QAtools but wanted to understand if there is a systematic computation of say a handful of variables that would give us a global representation of how well things worked for each case we run? Something that we could compare across our patients and even across data sets? Best, KZ ___ 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] QAtools error
Dear Freesurfer experts, I am attempting to use QAtools to retrieve QA measures for my subjects. I can obtain WM SNR/avg/sd, but it appears the structural segmentation table is from a previous version of freesurfer (as the file order is different) and doesn't appear to work with my subjects processed recently in v5.3. To fix this I would imagine one would need to create a new template off of a subject with the -gen-asegLUT flag or use the -asegLUT flag. Attempting to use -asegLUT flag with the ASegStatsLUT.txt results in: Processing each subcortical label ... mysubject has 35 outliers ... (With all structures as outliers, and without reporting the SNR/avg/sd for each segmentation) When attempting to write out a new segmentation table with the -gen-asegLUT flag the error I receive is: gawk: /usr/local/freesurfer/QAtools/QAtools_v1.1/gstd.awk:22: (FILENAME=- FNR=1) fatal: division by zero attempted (standard_in) 1: syntax error (standard_in) 1: syntax error The command is here: $QA_tools/recon_checker -s mysubject -asegLUT $FREESURFER_HOME/ASegStatsLUT.txt Am I going about this correctly? Best, KZ ___ 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] Editing ROI labels
Dear Freesurfer experts, My PI would like to know, when editing the ROI labels from the freesurfer color look-up table/aparc+aseg.mgz file with freeview voxel editor (at the end of -autorecon3), what commands need to be re-run to apply the changes to reflect the accurate volumetric data of each label? As, if I'm not mistaken, running -autorecon3 would overwrite all of the edits made at this point. Best, Kody J. Zalewski ___ 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] Stats file question
Hi Doug, I sincerely apologize for being unclear! I'm still relatively new to freesurfer and learning the ropes. I've attached the three aforementioned .stats files. The lh.aparc.stats and DKTatlas40.stats were generated from running recon-all. When comparing them it appears the grey matter volume data between the same ROIs can vary significantly. I have also been running the commands individually from the recon-all v5.3 dev table (listed here https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable). When I ran the mri_segstats command to generate the wmparc.stats file: mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject TB0204U_FREESURFER_THIRDRUN --surf-wm-vol --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt The cortical ROIs were listed alongside the white matter segmentations in wmparc.stats, and now have different grey matter volumes than either of the previous two .stats files, which has left me even more confused. Since these cortical volumes all differ from one another, it makes me wonder which .stats file has the most accurate cortical volumetric data. Best, Kody J. Zalewski Message: 4 Date: Wed, 27 May 2015 14:58:44 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Stats file question To: freesurfer@nmr.mgh.harvard.edu Message-ID: 556613e4.3060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed Can you list the 3 stats files you are talking about? I can't quite follow from below doug On 05/26/2015 02:21 PM, zal...@u.washington.edu wrote: Hello Freesurfer team, When generating the .stats files for grey matter volumetric data, this information appears in multiple places and I'm not sure which data I should be using for my final results. There appears to be cortical information generated in both the .stats file based off the DKT atlas and the l/rh.aparc.stats file. The information in these files is quite different from one another. Using the FreeSurferColorLUT.txt (as listed in the recon-all dev table) instead of WMParcStatsLUT.txt (which is used when running recon-all) in generating the mri_segstats wmparc.stats file also produces cortical volumetric data. This third set of data differs significantly from the DKT Atlas, and differs less-so from the cortical volumes produced in the aparc.stats file. Which of the .stats files containing grey matter volume data is most accurate? Best, Kody J. Zalewski ___ 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 lh.aparc.DKTatlas40.stats Description: Binary data lh.aparc.stats Description: Binary data wmparc.stats Description: Binary data ___ 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] Stats file question
Hello Freesurfer team, When generating the .stats files for grey matter volumetric data, this information appears in multiple places and I'm not sure which data I should be using for my final results. There appears to be cortical information generated in both the .stats file based off the DKT atlas and the l/rh.aparc.stats file. The information in these files is quite different from one another. Using the FreeSurferColorLUT.txt (as listed in the recon-all dev table) instead of WMParcStatsLUT.txt (which is used when running recon-all) in generating the mri_segstats wmparc.stats file also produces cortical volumetric data. This third set of data differs significantly from the DKT Atlas, and differs less-so from the cortical volumes produced in the aparc.stats file. Which of the .stats files containing grey matter volume data is most accurate? Best, Kody J. Zalewski ___ 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] Motion Correction with T2
Hello again Freesurfer team, Is it possible to perform a motion correction with only a T1 and a T2 scan, as my lab only has one available T1 scan per participant. Since the intensities of T1 and T2 are opposite of one another I've had no luck so far, but perhaps your team knows of a work-around. Best, Kody J. Zalewski ___ 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] Cortical volumes/ROI labelling question
Hello Freesurfer team, I've been previously learning freesurfer by going through the individual recon-all commands listed on the freesurfer website v5.3 table here: http://freesurfer.net/fswiki/ReconAllTableStableV5.3 and recently just ran through the recon-all autorecon steps 1, 2 and 3. Running the command individually as listed on the website: mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject TB0204U_FREESURFER_THIRDRUN --surf-wm-vol --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt This produces both cortical and subcortical volumetric data in the same wmparc.stats file. (attached to this email as wmparc.stats) Whereas, the default command from recon-all is: mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject TB0204U_FREESURFER_THIRDRUN --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv The resulting file is attached to this email as wmparc2.stats along with the DK40 stats. The only differences are the --brain-vol-from-seg flag (which doesn't seem relevant, based on the description of the flag), and the lookup table used in the generation of the wmparc.stats file. During the recon-all run, the wmparc.stats file only listed subcortical regions, whereas the DK40 atlas is the only source listing cortical volumes. While I would just use the DK40 atlas to retrieve this information, the problem here is that there appears to be a significant difference between the mm^3 volume of hemispherical cortical areas listed in the DK40 atlas compared to those produced when running the command with the flags. Unfortunately, I am not familiar enough with cortical volumes to recognize which estimate is more reasonable one. What .stats file or look-up table should I be using to obtain the most accurate cortical data? Also, when fixing errant ROI label voxels with freeview voxel editor, what commands need to be run post-editing to apply the corrections? I was under the impression that the aparc+aseg.stats file was edited when changing the ROIs. Although, I was rather confused when I went back and regenerated the aparc+aseg.mgz file and my edits were still present. Best, -Kody J. Zalewski wmparc.stats Description: Binary data wmparc2.stats Description: Binary data lh.aparc.DKTatlas40.stats Description: Binary data rh.aparc.DKTatlas40.stats Description: Binary data ___ 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] recon-all compared to dev table
Dear freesurfer team, I'm very new to freesurfer, and I am currently working my way through the recon-all dev table functions (listed here: http://freesurfer.net/fswiki/ReconAllDevTable) step-by-step in preparation for processing a large amount of participant volumetric data. While doing so I've noticed some inconsistencies between the dev table and the series of functions called by the recon-all command. For example: -The apas2aseg function listed in the dev table does not exist in my bin file (nor does it appear to be called by recon-all). -The cortical ribbon output occurs after the three cortical parcellation steps/creation of the anatomical.stats files (instead of prior to these steps like the dev table suggests) -The MNI intensity correction (the mri_nu_correct.mni function) is not called following the skull-stripping. I downloaded the latest version of freesurfer (5.3.0) last week so it should be up-to-date. Thank you for taking the time to answer my questions, -Kody J. Zalewski ___ 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.
