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Today's Topics:

   1. Re: Cortical thicknees normalization values (Douglas N. Greve)
   2. Re: Calculating group-wise Dice Similarity Coefficient and
      corresponding surface map (Douglas N. Greve)
   3. Re: smoothing volume data extracted using aparcstats2table
      (Douglas N. Greve)
   4. Hippocampal Subfield Definition Errors (Franchesca Kuhney)
   5. Re: Problem with mri_glmfit-sim (Douglas N. Greve)
   6. Re: recon-all soft errors (Douglas N. Greve)
   7. Re: mri_glmfit DOSS (Douglas N. Greve)
   8. Re: LGI FS 7.1 (Douglas N. Greve)
   9. Re: Can I extract GLM values? (Douglas N. Greve)
10. Re: fcseed-config (Douglas N. Greve)
11. Re: Help segmenting all subjects in a folder (Douglas N. Greve)
12. Re: Question about Extracting QDEC Results (Douglas N. Greve)
13. Re: Edit pial surface (Douglas N. Greve)
14. Re: Hippocampal Subfield Definition Errors
      (Iglesias Gonzalez, Juan E.)
15. Re: What is the relationship between qdec results and
      aparc.stats? (Douglas N. Greve)
16. Re: setwdelay error 1 weight (Douglas N. Greve)
17. Re: Transformation Applied to T1.mgz during recon-all
      (Douglas N. Greve)
18. Re: Visualizing specific cortical parcels in Desikan Killiany
      atlas (Douglas N. Greve)
19. Re: Freesurfer longitudinal stream error (Douglas N. Greve)
20. Re: LGI FS 7.1 (Del Re, Elisabetta)
21. Re: question about longitudinal data analyses (Douglas N. Greve)
22. Average intensity from functional image within a label along
      the surface (Erik Jahner)

----------------------------------------------------------------------

Message: 1
Date: Fri, 9 Jul 2021 12:40:13 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Cortical thicknees normalization values
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <f3f7c9b2-9e2d-80c3-4d5e-c4c92359d4e1@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

We generally do not normalize it by anything. ICV norm is not needed
because thickness does not scale with head size. Sometimes people will
normalize by mean thickness, but that changes the question being
answered, so that is more a question for you

On 6/24/2021 3:01 PM, Gabbo Ram?rez Garc?a wrote:
>
> ????????External Email - Use Caution
>
> ????????External Email - Use Caution
>
>
>
> Hi freesurfer user.
>
> I have been working with some cortical thickness values of a control
> group to test some changes related to cognitive training. However, I
> have been hesitating about whether I have to normalize the cortical
> thickness values (as happens with subcortical volumes and ICV) or not.
> I have read a little about it and I understood that I could use the
> ICV or/and mean cortical thickness, but I didn't find a specific
> criteria to do or not this normalization. Any clue, recommendation,
> explanation or paper about this will be very helpful.
>
> Thanks in advance.
>
> *or reposting?discussion?of this question.
>
> *Gabriel R.*
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1igRZreQyL28dpaDxcw1KUE3935aWbqlbZ8jIEL5JY7FolB-S-U_VYuvhI-5Zwj73nhgC-yUMsLNFXTFluiVPuSmaVXN_39-Fl9swxgpdrugnmgZcWEuaY_c1_qlT5n3npwt0ZxzDLdwQc_N9TsJzhh5fadopoPF69JY4lq0wrk290GbNgpWaY7WJ4J6b0HlMvdElGoKaR00AvVT9lr8sw_rI8ai-ICPblB-ChOhYFBVpX9kSY0-vkAa3uDoxaGaLdLPiZ4xv8LBhPTVAtlxy7Q/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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------------------------------

Message: 2
Date: Fri, 9 Jul 2021 12:43:20 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Calculating group-wise Dice Similarity
        Coefficient and corresponding surface map
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <bb42db88-e23f-2ff3-38b9-74e642ce77ec@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

try $FREESURFER_HOME//matlab/annotval2surfoverlay.m

On 6/25/2021 2:55 PM, Fischl, Bruce wrote:
>
> I guess doing it in matlab would be easiest
>
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Hye Min Shin
> *Sent:* Friday, June 25, 2021 1:24 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Calculating group-wise Dice Similarity
> Coefficient and corresponding surface map
>
> *????????External Email - Use Caution *
>
> Thank you for the response Bruce.
>
> I apologize for the confusion regarding surface map but what I was
> trying is that I wanted to create a surface file that contains dice
> coefficients for labels across the entire cortex. With your response,
> I think I can get the average dice coefficient for each label and
> hopefully create a surface map that visualizes dice coefficients on
> brain surface map.
>
> Would there be a way to create my own surface map with brain
> morphometry values that I created?
>
> Best,
>
> Julia Shin
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------

Message: 3
Date: Fri, 9 Jul 2021 12:55:10 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] smoothing volume data extracted using
        aparcstats2table
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <11dd28aa-57c5-c9e8-253b-8deaed88bbef@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Generally, you do not smooth it as averaging over the ROI is effectively
a type of smoothing. If you were to smooth prior to the averaging, you'd
get one area smearing into another.

On 6/28/2021 12:57 PM, Ryan Bell, Ph.D. wrote:
>
> ????????External Email - Use Caution
>
> Dear Freesurfer Experts,
>
> I am wondering whether the extracted ROI volume data acquired when
> using the command aparcstats2table needs to be smoothed?? I performed
> surface smoothing using surf2surf for cortical thickness data, but
> cannot find a way to smooth the volume data listed in
> aparcstats2table.? Is it recommended that I do not perform smoothing?
>
> Thank You,
>
> Ryan
>
> -----------------------------------------------------------------------------------------------
>
> Ryan Patrick Bell, Ph.D.
> Research Analyst, Department of Psychiatry & Behavioral Sciences
> 905 W. Main St., Suite 24-E
>
> Durham, NC 27701
>
> Phone: (919) 681-3495
>
> Email: ryan.bell@duke.edu <mailto:ryan.bell@duke.edu>
>
> Website: _*MailScanner has detected a possible fraud attempt from
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------------------------------

Message: 4
Date: Fri, 9 Jul 2021 12:06:14 -0500
From: Franchesca Kuhney <fkuhne2@uic.edu>
Subject: [Freesurfer] Hippocampal Subfield Definition Errors
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAKar3hdor6N2tH_Wjq1KyPT=A_PC=TfmYwAiizsX+1=B4OXpKw@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Hello,

I've run into an issue with the longitudinal hippocampus/amygdala
segmentation (segmentHA_T1_long.sh). All of the commands ran properly and I
got the outputs listed on the FreeSurfer wiki but, upon QAing the
segmentations, I realized that a few subjects hippocampal segmentations were
a poor fit. It appears that the segmentation includes their parahippocampal
gyrus. I'm wondering if you have any recommendations for how to fix these
either manually or automatically? Thank you!

Kindly,
Franchesca

*Franchesca Kuhney, M.A.* *(she/her)*
Clinical Psychology Doctoral Student
University of Illinois at Chicago
Behavioral Sciences Building | Rm 3019
1007 W. Harrison St. | Chicago, IL 60607

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------------------------------

Message: 5
Date: Fri, 9 Jul 2021 13:58:24 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with mri_glmfit-sim
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <b4cd8e63-a4ee-f2da-3014-a7c0c9ea2430@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

I think this might be a bug. You might be able to get around it by
adding --no-perm-resid as the last option. Why are you running your own
simulation instead of using the precomputed tables?

On 6/28/2021 1:38 AM, juergen.haenggi@upd.unibe.ch wrote:
>
> ????????External Email - Use Caution
>
> Dear Douglas
>
> please find the terminal output and the log files attached.
> when I run this command in FS 6.0.0, no error occurred
>
> thanks in advance
>
> cheers
> J?rgen
>
>
>
>> Am 27.06.2021 um 16:49 schrieb Douglas N. Greve
>> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>:
>>
>> Can you send the mri_glmfit.log file from your mri_glmfit run?
>> Can you run mri_glmfit-sim with --debug as the first option and
>> capture and send the output?
>>
>> On 6/23/2021 4:42 AM, juergen.haenggi@upd.unibe.ch
>> <mailto:juergen.haenggi@upd.unibe.ch> wrote:
>>>
>>> ????????External Email - Use Caution
>>>
>>> Dear FS experts
>>>
>>> I have run stats using mri_glmfit (FS 7.1.1 on Mac) with the
>>> following command
>>>
>>> mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd
>>> IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir
>>> --surf fsaverage lh --C IPS_2groups.mat --cortex
>>>
>>> and everything worked fine. When trying to run simulations with
>>> mri_glmfit-sim with the following command
>>>
>>> mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim
>>> mc-z 500 1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite
>>> --cwpvalthresh 0.25
>>>
>>> the following error occurred
>>>
>>> Loading y from
>>> /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
>>> error: mri_read(): couldn't determine type of file
>>> /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
>>> ... done reading.
>>> ERROR: loading y
>>> /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
>>>
>>> The entire output is shown below.
>>> I do not understand why after the ?y option in the command reported
>>> by FS in the terminal, i.e.
>>>
>>> mri_glmfit --C
>>> IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx
>>> --sim mc-z 500 1.302
>>> IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001
>>> --sim-sign abs --fwhm 14.598750 --fsgd
>>> IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask
>>> IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force
>>> --surf fsaverage lh white
>>>
>>> the input file (IPS_2groups_n135_lh_thickness.10.mgh) is missed and
>>> hence the following option ?perm-force is interpreted as input file.
>>>
>>> How can I fix this problem?
>>>
>>> Thanks in advance for any advise
>>> Regards
>>> J?rgen
>>>
>>>
>>> ---------------------------------------------------
>>> entire output:
>>>
>>> [upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi%
>>> mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim
>>> mc-z 500 1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite
>>> --cwpvalthresh 0.25
>>> cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd
>>> IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir
>>> --surf fsaverage lh --C IPS_2groups.mat --cortex
>>> SURFACE: fsaverage lh
>>> log file is
>>> IPS_2groups_n135_Thickness_LH.glmdir/lh_mc-z.abs_500p1.3.mri_glmfit-sim.log
>>>
>>> cd
>>> /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135
>>> /Applications/freesurfer/bin/mri_glmfit-sim
>>> --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim mc-z 500 1.302
>>> lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25
>>>
>>> FreeSurferEnv.csh 7.1.1
>>> Wed Jun 23 10:19:19 CEST 2021
>>> Darwin upddkp224.unibe.ch
>>> <http://secure-web.cisco.com/1kqev2VghLiWSg5kIlxOKq_VbJZc9JK-pk9pBXL8_xh9udahFBCv8EvuJ9GuriYfcowB1DAoh5MAMRkYqUO02V_5nmE4VP10JT85LV5FW_dqPd3gGa14VqqkgWLHu9xxCHFT7s8bFskBPK-8PML54WB77N_8bUtYd1r3Qh3VZu7eaRw1teNI4YSlpPAPOHZOvFY8TRdxlfSUjQd7VN9nd_7zJRz4srPlQzrTlohVaHWsmlRNB9lVm4YVYKBaKL7JtQp2863TnS1zUJjRGu3rV-A/http%3A%2F%2Fupddkp224.unibe.ch>
>>> 19.6.0 Darwin Kernel Version 19.6.0: Thu May? 6 00:48:39 PDT 2021;
>>> root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64
>>> jurgenhanggi
>>> setenv SUBJECTS_DIR /Applications/freesurfer/subjects
>>> FREESURFER_HOME /Applications/freesurfer
>>>
>>> Original mri_glmfit command line:
>>> cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd
>>> IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir
>>> --surf fsaverage lh --C IPS_2groups.mat --cortex
>>>
>>> DoSim = 1
>>> UseCache = 0
>>> DoPoll = 0
>>> DoPBSubmit = 0
>>> DoBackground = 0
>>> DiagCluster = 0
>>> gd2mtx = dods
>>> fwhm = 14.598750
>>> nSimPerJob = 500
>>> 1/1 Wed Jun 23 10:19:19 CEST 2021
>>> mri_glmfit --C
>>> IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx
>>> --sim mc-z 500 1.302
>>> IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001
>>> --sim-sign abs --fwhm 14.598750 --fsgd
>>> IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask
>>> IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force
>>> --surf fsaverage lh white
>>> INFO: ignoring tag Creator
>>> INFO: ignoring tag SUBJECTS_DIR
>>> INFO: ignoring tag SynthSeed
>>> simbase
>>> IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001
>>> FWHM = 14.598750
>>> gdfRead(): reading IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
>>>
>>> WARNING: carriage returns have been detected in file
>>> IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
>>> Was it created on a Windows computer?
>>> This may cause an error in reading the FSGD file.
>>> If so, try running:
>>> ? ? cat IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd | sed
>>> 's/\r/\n/g' > new.IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
>>> Then use new.IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
>>>
>>> INFO: gd2mtx_method is dods
>>> Reading source surface
>>> /Applications/freesurfer/subjects/fsaverage/surf/lh.white
>>> Number of vertices 163842
>>> Number of faces? ? 327680
>>> Total area ? ? ? ? 65417.000000
>>> AvgVtxArea ? ? ? 0.399269
>>> AvgVtxDist ? ? ? 0.721953
>>> StdVtxDist ? ? ? 0.195472
>>> Surface smoothing by fwhm=14.598750, niters=157.000000
>>>
>>> 7.1.1
>>> cwd
>>> /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135
>>> cmdline mri_glmfit --C
>>> IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx
>>> --sim mc-z 500 1.302
>>> IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001
>>> --sim-sign abs --fwhm 14.598750 --fsgd
>>> IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask
>>> IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force
>>> --surf fsaverage lh white
>>> sysname? Darwin
>>> hostname upddkp224.unibe.ch
>>> <http://secure-web.cisco.com/1kqev2VghLiWSg5kIlxOKq_VbJZc9JK-pk9pBXL8_xh9udahFBCv8EvuJ9GuriYfcowB1DAoh5MAMRkYqUO02V_5nmE4VP10JT85LV5FW_dqPd3gGa14VqqkgWLHu9xxCHFT7s8bFskBPK-8PML54WB77N_8bUtYd1r3Qh3VZu7eaRw1teNI4YSlpPAPOHZOvFY8TRdxlfSUjQd7VN9nd_7zJRz4srPlQzrTlohVaHWsmlRNB9lVm4YVYKBaKL7JtQp2863TnS1zUJjRGu3rV-A/http%3A%2F%2Fupddkp224.unibe.ch>
>>> machine? x86_64
>>> user ? ? jurgenhanggi
>>> FixVertexAreaFlag = 1
>>> UseMaskWithSmoothing ? ? 1
>>> fwhm ? ? 14.598750
>>> niters? ? 157.000000
>>> OneSampleGroupMean 0
>>> y
>>> /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
>>> logyflag 0
>>> usedti? 0
>>> FSGD IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd
>>> mask IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh
>>> maskinv 0
>>> glmdir (null)
>>> IllCondOK 0
>>> ReScaleX 1
>>> DoFFx 0
>>> Loading y from
>>> /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
>>> error: mri_read(): couldn't determine type of file
>>> /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
>>> ?? ... done reading.
>>> ERROR: loading y
>>> /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force
>>> [upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi%
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Message: 6
Date: Fri, 9 Jul 2021 14:01:36 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon-all soft errors
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0c0b8c15-adbe-840d-1b16-fa087f8b9791@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

On 6/29/2021 3:32 AM, Rosalia Dacosta Aguayo wrote:
>
> ????????External Email - Use Caution
>
> Dear Freesurfer team,
>
> I am inspecting the different participants I have run recon-all -all
> and I have found different errors I would like to discuss with you
> before proceeding as I am new with this software.
>
> 1. I have found dura at some regions of the brain. I should use gcut
> or delete voxels?
I've never used gcut, but deleting voxels will work
> 2. I have found discontinuity in GM and what I should do with this
> (attached photo 2)
Not sure what you are pointing to. Some of the problems may be in the
medial wall (which is not a problem).
> 3. In photo 1, not sure at some regions were to consider wm as it is
> not clear for me...any suggestion with this one? I think it should be
> done with cp, right?
I guess so. The data quality looks pretty low, so it might be hard to tell.
>
> Kind regards,
> Rosie
>
> *
> *
>
>
> _______________________________________________
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Message: 7
Date: Fri, 9 Jul 2021 14:05:31 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit DOSS
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <c4adbb10-3145-317e-a054-49015f7dcb73@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

You cannot use a DODS in this design as it tries to fit an offset and a
slope for each class, which can't be done when the class has only one
member. Try using DOSS instead. You should probably demean and rescale
the eTIV to be between 0 and 1.

On 6/29/2021 11:19 AM, Dr. Cornelius Kronlage wrote:
>
> ????????External Email - Use Caution
>
> Dear freesurfers,
>
> for a morphometry study, I am comparing a single subject at a time to
> a group of controls. I would like to include age, gender (as a
> continuous variable for the sake of simplicity) and eTIV as ?nuisance?
> regressors in the GLM. The FSGD looks like this:
>
> GroupDescriptorFile 1
> ?? ?Title SUBJECT1_vs_allControls
> ?? ?Class Test
> ?? ?Class Controls
> ?? ?Variables Age Gender eTIV
>
> Input SUBJECT1 Test 50 1 1497422.2500
> Input SUBJECT2 Controls 30 0 1709039.536815
> Input SUBJECT3 Controls 29 0 1423097.816203
> Input SUBJECT4 Controls 31 1 1524690.026713
> ...
>
> When I try to run mri_glmfit I get the following error even though I
> specify DOSS:
>
> $ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...]
>
> gdfRead(): reading SUBJECT1_vs_allControls.fsgd
> WARNING: variable 1 is "Gender" which is often a discrete factor
> ? The proper way to handle discrete factors is to create classes.
> ? See MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 Age 28.6875 6.36611
> 1 Gender 0.46875 0.499022
> 2 eTIV 1.51444e+06 125811
> Class Size and Means of each Continuous Variable
> 1 Test? 1? 50.0000?? 1.0000 1497422.2500
> 2 Controls 31? 28.0000?? 0.4516 1514993.8589
> ERROR: Class Test has 1 members. With 3 variables and using DODS, you
> need at least 4 members
>
> How do I get mri_glmfit to use DOSS, or do I have to specify the
> design matrix by hand in this case?
>
> Thank you!
>
> Best wishes
> Cornelius
>
>
> _______________________________________________
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Message: 8
Date: Fri, 9 Jul 2021 14:08:23 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] LGI FS 7.1
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <357d2e52-6e98-8a34-41f6-b4be9941d74d@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I'm not sure what you mean. Can you elaborate?

On 6/30/2021 5:05 PM, Del Re, Elisabetta wrote:
>
> ????????External Email - Use Caution
>
> ????????External Email - Use Caution
>
> Thank you so much.
> I am still in doubt as to whether adjust/normalize for brain volume or
> otherwise surface area before comparing groups.
> Thank you for your advise,
> best wishes,
> Elisabetta
>
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
> <dgreve@mgh.harvard.edu>
> *Sent:* Sunday, June 20, 2021 10:34 AM
> *To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] LGI FS 7.1
> The biggest changes are intensity normalization and highres support,
> but many more changes. See the release notes
> *MailScanner has detected a possible fraud attempt from
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> MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
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>
>
> On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:
>>
>> ????????External Email - Use Caution
>>
>> ????????External Email - Use Caution
>>
>>
>> Dear FS team,
>> what are differences if any between LGI in FS 5.3 and 7.1?
>> Thank you so much,
>> best wishes,
>> Elisabetta
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> https://secure-web.cisco.com/1sLeUzUQ901lGnNjwPD2kwN8sTPX4PBy7pYeeGHSUcTGTpyPQVYe6iXhPFScxxTKPHCSwO_YuHw6MKNJGzgJtS8uEnX2_kvT_nS9W1TOItISbcDoX29GssQprhBVXb9Cs5WdVi3awt3zBuAJ_gRYP4MwqTriJGGx9WOsGmUvc76DqpyhV4KQNFD3srHa6uD7lW3hKBSgSJiJLglZTpqqVChh9eSz28PfY9xhZTv4bkkSxY8nPaqL7gZzD9sbN1IrCNI3hQgR73dSx9UJA48RxEg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer <https://secure-web.cisco.com/1O3Kk0oSUij-GUZ_t2ELwmiO_yM7wDzhqK6bEVa1ZEgIeAZglJL_GN77yf0pvGqCu7i3Lk4gFOEuoHClcxXtgHrFCjnez5gWSlgQ1qlXhVFJOWVLu2x2ysYRnQ6JjLm5dgLlIRNPTj3-bWa01XRB-GOpJDsOhGl5EP1UfXOYyKMk6QRZWwAVDFlxkGhwt86_DHUcau5joPYmR8OWurXcd8vBtr9GnX3lMlg313hN6E39aDhhm8vCSbBgS7WIME-hKXZzlzMpQTzPg4NtZT0VjIQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__secure-2Dweb.cisco.com_1sLeUzUQ901lGnNjwPD2kwN8sTPX4PBy7pYeeGHSUcTGTpyPQVYe6iXhPFScxxTKPHCSwO-5FYuHw6MKNJGzgJtS8uEnX2-5FkvT-5FnS9W1TOItISbcDoX29GssQprhBVXb9Cs5WdVi3awt3zBuAJ-5FgRYP4MwqTriJGGx9WOsGmUvc76DqpyhV4KQNFD3srHa6uD7lW3hKBSgSJiJ
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>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 9
Date: Fri, 9 Jul 2021 14:11:37 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Can I extract GLM values?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <9659cb84-2f2c-7359-1dce-0042b7e83bf0@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

There should be a file called something like gamma.table.dat
This is a text file with the differences for each ROI and contrast.

On 7/1/2021 4:39 AM, Thalhammer, Melissa wrote:
>
> ????????External Email - Use Caution
>
> Dear FS experts,
>
>
> I have run mris_preproc and mri_glmfit for group analysis as described
> in the docs. My current project deals with the analysis of cortical
> thickness of preterm- vs. term-born adults and I want to correlate the
> difference in cortical thickness between those two groups with gene
> expression data. Thus, I would need the group difference ROI-wise as
> values in a spreadsheet/text file to perform correlation lateron. I
> have used the following code with the --table flag and have used
> cortical thickness data extracted with aparcstats2table as input.
>
> Is there a way to extract the ROI-wise group difference, corrected for
> the covariates included into my GLM model?
>
>
> Best,
>
> Melissa Thalhammer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 10
Date: Fri, 9 Jul 2021 14:42:17 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] fcseed-config
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <182b9297-50d8-2984-f04e-de25a51bd983@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

you should not pass it a label. If you look at the help,
Functional ROI-based options
? -roi fcconfig : as created by funcroi-confg

On 7/1/2021 10:58 AM, Nasiriavanaki, Zahra wrote:
> Hello Freesurferers,
>
> I?m trying to use a functional label (extracted from task functional
> BOLD data), as a seed for functional connectivity.
> I tried to use the fcseed-config with -roi , but when I ran the
> fcseed-sess, I got this error: ?If: expression syntax error?.
> Could you please let me know what the problem is?
>
>
> fcseed-config ?-roi ${label}.label? -fcname ${label}.dat -fsd rest
> -rlf restruns -mean -cfg ${label}.config -force
>
> fcseed-sess ?-s ${subj} ? -d ../ ?-cfg /${label}.config
>
> Thanks,
> Mona
>
>
> *Zahra (Mona) Nasiriavanaki, M.D.*
> Postdoctoral Research Fellow
> Department of Psychiatry
> Massachusetts General?Hospital
> 149 13th Street, 149-2615
> Boston, MA, USA, 02129
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 11
Date: Fri, 9 Jul 2021 14:43:39 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Help segmenting all subjects in a folder
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <458d1fab-5bad-cee0-e842-8d7524d3ab08@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

That does not apply to the recon-all command, only to
mri_segment_hypothalamus_subunits

On 7/1/2021 12:23 PM, g.toniol@libero.it wrote:
>
> ????????External Email - Use Caution
>
> Hello FreeSurfer Developers,
>
> Thank you for your work !
> I successfully set up Freesurfer and ran a test on my computer, and I
> am now?attempting to?run recon-all on all subjects in a folder
> ("/home/users/s/saccaro/Groupe_0"?in the example script below). I run
> the analysis on a HPC (SLURM system).
>
> I found that, concerning the recon-all command, "If no name is given
> after --s, the code will be run on ALL subjects in $SUBJECTS_DIR
> <https://secure-web.cisco.com/1cAYZmFGVfas4DCf91-Y9WZa9anAVybKAgr13rFXfcD8BmuTPUSvDFohmKg6XCOHsIyMh3GxdvII3R4KsnUNvVgmkFYaXaLUrV6D4KS_FHQoG-jh3udJfVenKYjfGnQ52GhpYoVVrX0tBf7dYQrUolGWmFw6e6_WhYzueJZGR4-f7wZgN7ElCR8p-E0JP_iMzorzjxp4ZS3pmsDJZJvZJBPtOe4ViP3yDrkR8Q0-xSgssKu5gO4tvQffgOtxO6IJ39HSHMy99mPGWxaH3WxM5sg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHypothalamicSubunits>."
> but I do not find information on how this could work also for the
> previous step, mri_convert: is there a way to submit a job to segment
> all subjects in the folder "Groupe_0", and not just S001 (in the
> example below)? All folders are structured as follows:
> /S@@@/scans/struct/@@@@@@.nii .
>
> I am new to Freesurfer and I apologize if my question is naive but I
> cannot find a solution in any of the online resources.
>
> Thank you very much for your time!
> Best,
>
> Giorgio
>
> *- Script, without SBATCH settings (I join the full version):*
>
> module load FreeSurfer/6.0.0-centos6_x86_64
> source /home/users/s/saccaro/SetUpFreeSurfer.sh
> FSDIR="/home/users/s/saccaro/Groupe_0"
>
> mksubjdris ${FSDIR}/S001;
>
> mri_convert -i
> ${FSDIR}/S001/scans/struct/s44891-153636-00001-00192-1.nii -o
> ${FSDIR}/S001/scans/struct/s44891-153636-00001-00192-1.mgz
>
> recon-all -all -s S001
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 12
Date: Fri, 9 Jul 2021 14:45:05 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Question about Extracting QDEC Results
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0dc4dedb-6590-34a0-7ee9-3e8e84533365@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

which results? sig maps (and other maps) are surface overlays. You can
convert them to nifit format, but they will still be surface overlays
(so you would not view/analyze them in FSL or SPM)

On 7/1/2021 9:12 PM, Sonya Gupta wrote:
>
> ????????External Email - Use Caution
>
> Hi,
> Hope you are having a wonderful evening!
> I was wondering, is there a way to extract results from QDEC as a
> NIFTI file? If not, in what format can you the extract QDEC results?
>
> Thank you!
>
> Sincerely,
> Sonya
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 13
Date: Fri, 9 Jul 2021 14:46:51 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Edit pial surface
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <3f7fd34c-e4af-ccab-5610-d0320a2465f8@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

You can use the reposition surface tool in freeview. Just be careful
that you don't overwrite it if you re-run

On 7/2/2021 3:37 AM, Rosalia Dacosta Aguayo wrote:
>
> ????????External Email - Use Caution
>
> Dear Freesurfer's experts,
>
> I wonder if there is any chance to correct the pial surface when it
> does not cover entirely certain regions of GM, such for example,
> orbital frontal cortex
>
> Kind regards,
> Rosie
>
> *
> *
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------

Message: 14
Date: Fri, 9 Jul 2021 18:47:29 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal Subfield Definition Errors
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <7164D392-D7D8-43A9-9D0C-6E143E9A4C9D@mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"

Dear Franchesca,
Could you please attach some images illustrating the problem?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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On Jul 9, 2021, at 13:06, Franchesca Kuhney <fkuhne2@uic.edu <mailto:fkuhne2@uic.edu>> wrote:

        External Email - Use Caution

Hello,

I've run into an issue with the longitudinal hippocampus/amygdala segmentation (segmentHA_T1_long.sh). All of the commands ran properly and I got the outputs listed on the FreeSurfer wiki but, upon QAing the segmentations, I realized that a few subjects hippocampal segmentations were a poor fit. It appears that the segmentation includes their parahippocampal gyrus. I'm wondering if you have any recommendations for how to fix these either manually or automatically? Thank you!

Kindly,
Franchesca

Franchesca Kuhney, M.A. (she/her)
Clinical Psychology Doctoral Student
University of Illinois at Chicago
Behavioral Sciences Building | Rm 3019
1007 W. Harrison St. | Chicago, IL 60607
[https://secure-web.cisco.com/1puxmEK3mDm56IT5JV-3zOLSqMv5RYqFgYmoHYrQAp5MYBlH0FXgFmM2N6W2VgtUPqMnfqlwxhCUv48gthl3zpOFiFLDXBi-4UJn9X_iohYJ1MZ77rnkRSf-6io9SHkp51H6LTDgc9AVbUnDsOaOpjELnIyceWsALuSm9SvfwsWWxk2Fgy5XW_lQaQWtUnrvFhp5lGHL-Us4-ypqNv2jHbdT6cj1v1zyi-_8nePwm054SFDv4xbrcB67amiyHtbWyZra43v0abbt1OA_yPlZbbQ/https%3A%2F%2Fdrive.google.com%2Fa%2Fuic.edu%2Fuc%3Fid%3D1R1NXIxIFqUxTPkk1dgc36H1tbzYr63aH%26export%3Ddownload]
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------------------------------

Message: 15
Date: Fri, 9 Jul 2021 14:50:39 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] What is the relationship between qdec
        results and aparc.stats?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <4190b001-41fc-3d7a-acbd-5f43e8e0a20c@mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

ROI-wise and vertex-wise analyses are different and may give different
results. The vertex-wise analysis looks at individual vertices whereas
ROI-wise averages over all the vertices. It is possible (even expected)
that averaging over all vertices will reduce the variation and give
stronger statistics than vertex-wise.

On 7/2/2021 10:07 AM, Satoko KINA wrote:
>          External Email - Use Caution
>
> Hello Freesurfer Developers,
>
>
> As a result of whole-brain analysis using qdec, specific regions with significant differences between the two groups were depicted (e.g., paracentral cortical thickness).
> Based on this result, we compared the paracentral region on the Desikan-killiany atlas from aparc.stats between the two groups, and found significant differences not only in CT but also in items rejected by qdec (e.g., curv). How should we interpret this result? Which result is more reliable? Can we consider the result of the analysis focused on a narrow region of each ROI as a more detailed result because qdec is a whole brain analysis?
> I am not familiar with statistics, so please forgive me if this is a misguided question.
>
> Thank you for help!
>
>
> Satoko
>
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
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------------------------------

Message: 16
Date: Fri, 9 Jul 2021 14:54:31 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] setwdelay error 1 weight
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <121a2227-8839-737f-9357-2b0da91e484d@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

By my count, you entered 36 weights. I'm not sure why it says you only
entered 1, but try the correct number of weights first and see if the
problem goes away

On 7/3/2021 2:08 PM, Marilena Wilding wrote:
>
> ????????External Email - Use Caution
>
> ????????External Email - Use Caution
>
> Dear Freesurfers,
>
> for my FIR model I?d like to use the -setwdelay option in the
> mkcontrast-sess command.
>
> My command looks like this:
>
> mkcontrast-sess \
>
> -analysis FIR_group_20-lh -contrast global-v-local \
>
> -a 2 -c 1\
>
> -setwdelay
>
> When I run this the promt appears for the delay weights. But when I
> enter them, I always get an error:
>
>
> mkcontrast-sess -analysis FIR_group_20.lh -contrast global-v-local -a
> 2 -c 1 -setwdelay
>
> INFO: Found 2 Non-Null Conditions
> INFO: Found 29 Delays
> Condition Weights: -1.00000000000000000000 1.00000000000000000000
> ###################################
> ### Enter 29 Delay Weights (Return)
> 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> ERROR: entered 1 weights, needed 29
>
>
> I'm entering 29 values (I want to include only the first seven TPs)
> but apparently only 1 value is detected.
>
> Could you please help me? I'm really out of ideas here.
>
>
> Thanks a lot in advance!
>
>
> Marilena
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------

Message: 17
Date: Fri, 9 Jul 2021 14:59:24 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Transformation Applied to T1.mgz during
        recon-all
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <b385a808-c663-02f1-0210-a1321b041f61@mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

We refer to this operation as "conforming".
This page might help
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On 7/4/2021 4:39 PM, Alexander Rockhill wrote:
>???????? External Email - Use Caution
>
> Hello,
>
> ?? I am trying to replicate the processing steps that occur between
> when a T1 is given as input to recon-all and the T1.mgz that is stored
> in the $SUBJECTS_DIR/$SUBJECT/mri directory for mne-bids and dealing
> with mne's internal dependency on the surface RAS coordinate frame.
>
> ?? It is my impression that 1) the image is resampled to 256 x 256 x
> 256 and then 2) the image is reoriented to head-first supine aka LIA
> aka scanner space. But when I replicate these steps using nibabel, the
> affine is off by a rotation and translation:
>
> T1.mgz
> ------
>
> ????? [[ -1.??????? ,? -0.00000015,? -0.00000003, 132.77600098],
> ?????? [? 0.00000003,?? 0.00000001,?? 1.??????? , -94.00223541],
> ?????? [ -0.00000002,? -1.00000012,? -0.00000001, 149.55487061],
> ?????? [? 0.??????? ,?? 0.??????? ,?? 0.??????? ,?? 1.??????? ]]
>
> orig resampled and translated
> -----------------------------
>
> ????? [[ -0.99995208,? -0.00905184,?? 0.00373623, 164.44344257],
> ?????? [? 0.00337327,?? 0.03978604,?? 0.99920255, -98.49012464],
> ?????? [? 0.00919327,? -0.9991672 ,?? 0.03975359, 141.93864847],
> ?????? [? 0.??????? ,?? 0.??????? ,?? 0.??????? ,?? 1.??????? ]]
>
> orig to T1.mgz transform affine
> -------------------------------
>
> ????? [[? 0.99995203,? -0.00337331,? -0.00919312, -30.68693093],
> ?????? [? 0.0037362 ,?? 0.99920251,?? 0.03975359,? -1.8476189 ],
> ?????? [? 0.00905186,? -0.03978605,?? 0.99916736,?? 2.32735433],
> ?????? [? 0.??????? ,?? 0.??????? ,?? 0.??????? ,?? 1.??????? ]]
>
> Since there are off-diagonal entries in the last affine, I assume
> there is some kind of rotation, and since there are non-zero entries
> in the last column, I assume there is some kind of translation as
> well. I am not sure what either of those would be from so any advice
> or help would be appreciated.
>
> Alex Rockhill
> PhD Candidate University of Oregon
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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------------------------------

Message: 18
Date: Fri, 9 Jul 2021 15:43:26 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Visualizing specific cortical parcels in
        Desikan Killiany atlas
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <0a552541-1231-e345-e212-8279b41fecb5@mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

In FreeView, go to "View/Edit". From the resulting interface, you can
turn on and off any parcellations you want.

On 7/5/2021 1:04 PM, Ellen Ji wrote:
>          External Email - Use Caution
>
> Dear experts,
>
> I have a basic visualization question.
> I would like to create a surface brain figure with specific cortical
> parcels colored. Similar to
> https://secure-web.cisco.com/1DryTPj2WrD-LULa8TF6HVh2xwKTLAaWDFvIpAUrs4z6O2VOFttAjezDQX2aR4Z5m6bFRIWk8l6q3Kc0B4K1EjsGa3Ps7AUkb5SPODPx-r-FwnmCtHYHHKbdbpiaWUNhY_vlBvQaG-4Cl9kGxomgOLjtwUjpfxAwjLULtd8raS9pKKnnCsUkx0wW3RSuyX62NEemue5GJ8QZ5J46l4PfzCFjifys8EQeNVKxstOck3xiE-BXhju-kVWs7GQxLXjjk6zMrtaHPswi0sl3CPcqM2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FOutputData_freeview%3Faction%3DAttachFile%26do%3Dget%26target%3Dgood_output_aparc_crop.png
> but not with ALL parcels in the atlas selected.
>
> I know that I can go into a subject folder and load this freeview -f
> surf/lh.pial:annot=aparc.annot in order to see the entire Desikan
> Killiany atlas. However, I would like to select 4-5 rois.
>
> What's the best way to do this? It won't be related to any results and
> doesn't need to be from a particular subject's brain (can also be
> fsaverage). It's purely to highlight some cortical parcels for
> visualisation purposes.
>
> Thanks,
> Ellen
>
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------------------------------

Message: 19
Date: Fri, 9 Jul 2021 15:54:11 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer longitudinal stream error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <ff28aa5e-6733-0b52-842b-db29d496e872@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Try running it without the -parallel flag. If you want to use multiple
cores, then add -threads N (N= number of cores)

On 7/6/2021 4:29 AM, Susanne Gelli?en wrote:
> ??????? External Email - Use Caution
>
> Dear FreeSurfer Developers,
> I am processing MRI data using the freesurfer processing stream with
> two timepoints. I already executed the individual
> freesurfer-processing for each subject and timepoint and also the
> recon-all -base step. All finished without errors.
> When running the recon-all -long command, the processing stream exits
> at the same step in the script for all subjects and timepoints. I
> cannot identify a particular error message (ony at the end the script
> says exited with errors and no stats files are produced).
> ?I am using freesurfer 7.1.1 on an iMAc with macOS Catalina.
> Please find attached the recon-all log files for the longitudinal
> streams (2 folders with ?long? in the foldername) as well as for the
> preparation steps.
>
>
> Thank you.
>
>
>
>
> ---------------------------------------------------
>
> PD Dr. med. Susanne Gelli?en
>
> Department of Diagnostic and Interventional Neuroradiology
> University Medical Center Hamburg-Eppendorf
> Martinistra?e 52, 20246 Hamburg
> E-mail: s.siemonsen@uke.de
>
>
>
> --
>
> _____________________________________________________________________
>
> Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen
> Rechts; Gerichtsstand: Hamburg |
> http://secure-web.cisco.com/1HvVVbdMRr6qAu-L5y0c3HUFOZFKnzwzd2mFmsc4xoj1PMvHBZwQvrGMpUgr9mfBpN5hjM2R9dTml5iZZwEVwt-nEs4X5Z7IMAiBjsdv05MYZShXijGytKC09fYoZNsuKkkeCWhAZFMDOzCIyzaPUqFtCIzEWdphDQC89YcffIRfKfjMomVcKnc0J1ACVq4R4QeNFoo1P_nAX6nwpuILDzsXgN5-9GPacTKJvBBEAE9fEQ43-90fE5pf1DXRrMvh2hGS5qwFSjGaBGDs0vRV5vyNSYQm9l2KixSaD6hRT9ag/http%3A%2F%2Fwww.uke.de
> <http://secure-web.cisco.com/1HvVVbdMRr6qAu-L5y0c3HUFOZFKnzwzd2mFmsc4xoj1PMvHBZwQvrGMpUgr9mfBpN5hjM2R9dTml5iZZwEVwt-nEs4X5Z7IMAiBjsdv05MYZShXijGytKC09fYoZNsuKkkeCWhAZFMDOzCIyzaPUqFtCIzEWdphDQC89YcffIRfKfjMomVcKnc0J1ACVq4R4QeNFoo1P_nAX6nwpuILDzsXgN5-9GPacTKJvBBEAE9fEQ43-90fE5pf1DXRrMvh2hGS5qwFSjGaBGDs0vRV5vyNSYQm9l2KixSaD6hRT9ag/http%3A%2F%2Fwww.uke.de>
> Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Joachim
> Pr?l?, Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
> _____________________________________________________________________
>
> SAVE PAPER - THINK BEFORE PRINTING
> _______________________________________________
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Message: 20
Date: Fri, 9 Jul 2021 20:03:42 +0000
From: "Del Re, Elisabetta" <Elisabetta_DelRe@hms.harvard.edu>
Subject: Re: [Freesurfer] LGI FS 7.1
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <DF79C969-0E4C-4E1B-9BB9-7676F066E97F@hms.harvard.edu>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

Would you normalize for differences in head size by adjusting for eTiV or total surface area?
Thank you so much,
Elisabetta

Sent from my iPhone

On Jul 9, 2021, at 2:08 PM, Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

I'm not sure what you mean. Can you elaborate?

On 6/30/2021 5:05 PM, Del Re, Elisabetta wrote:

        External Email - Use Caution

        External Email - Use Caution

Thank you so much.
I am still in doubt as to whether adjust/normalize for brain volume or otherwise surface area before comparing groups.
Thank you for your advise,
best wishes,
Elisabetta

From: freesurfer-bounces@nmr.mgh.harvard.edu <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu><mailto:dgreve@mgh.harvard.edu>
Sent: Sunday, June 20, 2021 10:34 AM
To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] LGI FS 7.1

The biggest changes are intensity normalization and highres support, but many more changes. See the release notes
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On 6/9/2021 10:17 AM, Del Re, Elisabetta wrote:

        External Email - Use Caution

        External Email - Use Caution

Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta

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Message: 21
Date: Fri, 9 Jul 2021 16:04:21 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] question about longitudinal data analyses
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <b38582b0-0cfb-7805-79d5-8a59debc92dc@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

On 7/9/2021 11:44 AM, Ritobrato Datta wrote:
>
> ????????External Email - Use Caution
>
> Hi All,
>
>
> I have the following data ?
>
> I have 205 subjects - each subject was imaged at 3 timepoints
> (baseline, followup 1 and followup 2)
>
> The 205 subjects are split in two treatment arms with 100 subjects in
> the first one and 105 subjects in the second one.
>
> For each timepoint, I have created FA maps in their native diffusion
> space.
>
> I have also extracted the mean FA maps for 187 ROIs using mri_segstats.
>
> For each timepoint, I have saved the results as a matrix (FA in 187
> ROIs x 205 subjects) in a text file.
>
> So I have three files for the three timepoints.
>
> I have the age and cognitive score for each subject at each timepoint.
> And their gender.
>
> I want to answer the following questions ?
>
> 1. Do the baseline FA correlate with the corresponding cognitive
>     score at baseline ?
>
This is a straight forward group analysis, so see
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples (maybe the Two
Groups (1 Factor, Two Levels), One Covariate
<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G1V>)
>
> 1. I am interested in testing whether the FA?changed significantly
>     across the different timepoints and does that relate to the change
>     in the cognitive score
>
See MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
>
> 1. Is there an effect of treatment on this change in FA across time ?
>
Also see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
>
> Can you please suggest what programs in freesurfer will allow me to
> test these questions on both voxelwise and ROI wise ?
>
>
> Many thanks for your help and guidance,
>
>
> Regards
>
>
> Rito
>
>
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> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Message: 22
Date: Sat, 10 Jul 2021 04:47:54 +0000
From: Erik Jahner <eej_734@usc.edu>
Subject: [Freesurfer] Average intensity from functional image within a
        label along the surface
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <ACA3FA8D-E960-4619-A874-345BBC467EC2@usc.edu>
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        External Email - Use Caution

I am interested in obtaining the average intensity within a label from each frame of a functional image that has been smoothed on the surface (I have generated the label). However, the functional connectivity pipeline seems to use only volume based seeds. It seems to me that in using the FreeSurfer software we would want to take advantage of the surface based smoothing and not return to getting the average of voxels in aparc+aseg.

(1) Am I incorrect in my thinking here?

(2) Is there a way to get the mean intensity of a label (I have created) at each frame along the surface to get a timcourse for a particular region?

I see there is a way to do this with anatomical features such as thickness, but I do not see a way to do this with functional data across frames for signal intensity.

Thanks
~Erik Jahner

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End of Freesurfer Digest, Vol 209, Issue 11
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