Message: 13
Date: Thu, 16 Jul 2020 10:19:32 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] PETSurfer analysis question
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <d56acc7d-3273-4f40-ed17-570a893b26a3@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

The NoPVC and SGTM values are reasonable. The MG value is pretty crazy.
I don't put stock in MZ. Is the MG value much higher than SGTM in other
ROIs? What is your mri_gtmpvc command?

On 7/16/2020 4:38 AM, Ferraro, Pilar wrote:

????????External Email - Use Caution

Hi Freesurfer experts,

I?ve run a PETSurfer analysis in order to compare mean?uptake values
of ROIs obtained with different methods: No PVC, SGTM, MG and MZ.
However, I?ve now extracted the mean values and they are extremely
heterogeneous.
As an example, the same ROI (lh banks of the superior temporal sulcus)
has the following uptake values:

No PVC= 1.709
SGTM= 2.495
MG= 23.847
MZ= 15.564

I?m particularly worried for the huge difference between noPVC - SGTM
values and MG-MZ values.

Any advice? I wonder whether this finding is normal or there is
something I?ve missed.

Many thanks,

Pilar

Il giorno 15 lug 2020, alle ore 6:00 PM,
freesurfer-request@nmr.mgh.harvard.edu
<mailto:freesurfer-request@nmr.mgh.harvard.edu> ha scritto:

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Today's Topics:

??1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run
?????for some subjects (Douglas N. Greve)
??2. Re: mri_fieldsign error (Douglas N. Greve)
??3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan)

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

Message: 1
Date: Wed, 15 Jul 2020 11:12:21 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra
fails to run for some subjects
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <beb084b0-fe6b-c8a2-c0a5-e8bcc92769b6@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Can you send the recon-all.log file for some of the failures?

On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote:

????????External Email - Use Caution

Dear list,

As described by others on this list, recon-all with Freesurfer 7.1 on
a Mac operating system seems to fail for around 10% of the subjects.

The following solution was offered:

sudo curl
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init
?-o rca-long-tp-init
sudo chmod +x rca-long-tp-init
However, this did not solve the problem for me.

I re-ran recon-all for the same subjects, but it still failed, some of
them at the following step:

"#######################################
GCADIR /Applications/freesurfer/average
GCA RB_all_2020-01-02.gca
GCASkull RB_all_withskull_2020_01_02.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /Applications/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################"

It simply stopped running there.

Others did finish running, but instead got a segmentation fault error.

What could I do? I have Mac High Sierra.

Annelies

Annelies van't Westeinde?| PHD Candidate
Department of Women's and Children's Health | Karolinska Institutet
171 77 Solna | Karolinskav?gen 37A
+46 760967499
annelies.vant.westeinde@ki.se | ki.se <http://ki.se/en/startpage>
______________________________________
Karolinska Institutet ? a medical university

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Message: 2
Date: Wed, 15 Jul 2020 11:14:53 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_fieldsign error
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5364c956-1d58-e69d-5635-6fde5dd41c91@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I don't know what is going wrong here. One simple thing to check is to
make sure that all the input files have the same number of vertices as
the surface. If that is the case, then upload the subject and input
files using the instructions below

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log? into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.

On 7/15/2020 11:07 AM, Xiaomin Yue wrote:

????????External Email - Use Caution

Hi All,

Just in case the below poster was missed.

Thanks,

Xiaomin

*From: *Xiaomin Yue <mailto:yuexm@hotmail.com>
*Sent: *Saturday, July 11, 2020 1:43 PM
*To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *[Freesurfer] mri_fieldsign error

*????????External Email - Use Caution *

Hi Doug,

I used FS 7.1 under WSL to analyze retinotopy data.? Since the ring
and wedge were presented at a different frequency, the data had to be
analyzed separately for each condition.? To get the field sign, I had
to use the mri_fieldsign function to combine polar and eccen data.
However, an error happened with running mri_fieldsign: ?Segmentation
fault????? (core dumped)?.? The following is the command-line output.

Thanks for your help!

Xiaomin

cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala

cmdline mri_fieldsign --fs
LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar
LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz
LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s
LOO --hemi rh --sphere

sysname? Linux

hostname DESKTOP-SVDQE4Q

machine? x86_64

user???? xiaominyue

eccen real
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz

eccen imag
../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz

polar real LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz

polar imag LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz

patch???? (null)

subject???? LOO

hemi??????? rh

fwhm??????? -1.000000

nsmooth???? -1

fieldsign LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz

usenew????? 1

Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere

Using spherical coordinates

Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot

reading colortable from annotation file...

colortable with 36 entries read (originally
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Complex

Ripping Zeros

Rot (rad): 0 0

surfer: compute_fieldsign2()

dthresh = 1.5

shape = 1

nvertices = 153801

??? 0???? 0 45452?? 0.03? 33.2224

1018? 1000 39160? 21.33? -18.3959

2055? 2000 44734? 43.26? 33.0783

3148? 3000 49793? 65.38? 0.653687

4344? 4000 38626? 88.16? 16.7555

5529? 5000 54149 110.12? -4.90118

6706? 6000 61599 133.36? -5.74607

7971? 7000 50134 155.88? -17.5589

9165? 8000 34182 178.05? -18.9387

10591? 9000 59682 200.70? -4.60514

12034 10000 63856 223.18? -4.4884

13297 11000 41007 245.62? 27.3489

14938 12000 27365 267.70? -1.40077

16684 13000 23615 289.10? -0.518007

18048 14000 47088 309.37? 18.7017

19798 15000 21060 330.11? 15.9458

21681 16000 33067 350.27? -11.1953

23173 17000 28744 371.48? -6.18747

25112 18000 27738 392.41? -6.93845

26953 19000 20538 414.47? 2.99349

28903 20000 80583 435.98? -0.338512

30319 21000 16251 459.83? -45.2313

32174 22000 17139 483.36? -2.31642

34093 23000 13307 507.02? 19.1461

36170 24000 17826 530.65? -10.7575

37683 25000 69324 555.78? -6.17011

39666 26000 14043 583.29? -10.5151

41746 27000 76017 609.92? -0.0112556

43986 28000 84646 636.28? 1.24722

46088 29000 9763 664.26? 12.7035

48326 30000 92161 694.30? 2.03416

50431 31000 99884 724.91? 1.20525

./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault?????
(core dumped) mri_fieldsign --fs
$line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz --polar
$line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz
$line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz
../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz
--s $subjname --hemi $hemi --sphere

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Message: 3
Date: Wed, 15 Jul 2020 15:39:08 +0000
From: "O'Dell, Ryan" <ryan.odell@yale.edu>
Subject: [Freesurfer] Extracting PET Binding Values from Inflated
Surface
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BN8PR08MB5825811A87A2758B0DDC2D25F57E0@BN8PR08MB5825.namprd08.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

???????External Email - Use Caution

Hi Doug,

I have a question surrounding our attempts to extract PET binding
values (BPND/DVR) which have been first transformed into FS subject
space, mapped to the cortical surface using mri_vol2surf (signal
averaged over the middle 80% of the cortical ribbon), and then
displayed on the inflated hemisphere surfaces.

We would like to extract the average binding values from the cortical
surface ROIs using the Desikan-Killiany atlas, but are unsure how to
go about this. Is there a simple way to use aparcstats2table or a
similar command to extract average values from surface ROIs as
defined by the ?h.aparc.annot file?

Thanks!

Ryan O'Dell MD/PhD
PGY4 Psychiatry Resident, Yale University
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Message: 14
Date: Thu, 16 Jul 2020 17:57:28 +0200
From: Knut J Bjuland <knutjorgen@outlook.com>
Subject: Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR:
Number of filenames for --iscalein should agree with number of init
LTAs (--ixforms)! worked in fs6
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, "Douglas
N. Greve" <dgreve@mgh.harvard.edu>
Message-ID:
<DB6PR05MB3494D92A68AF36388DFFCF6EC37F0@DB6PR05MB3494.eurprd05.prod.outlook.com>

Content-Type: text/plain; charset="windows-1252"

External Email - Use Caution

Thanks
Sure,

Here is the log file.

Knut J?rgen

On 16/07/2020 16:12, Douglas N. Greve wrote:

Can you send the log file?

On 7/15/2020 1:51 PM, Knut J Bjuland wrote:

????????External Email - Use Caution

Dear freesurfer experts

I was able to run the same subects on the longitudinal stream using
FS 6 , but when I use FS7.1 I got this error

RROR: Number of filenames for --iscalein should agree with number of
init LTAs (--ixforms)!
ERROR:
@#@FSTIME ?2020:07:15:18:43:31 longmc N 5 e 1.75 S 0.47 U 0.15 P 35%
M 2444 F 88 R 26962 W 0 c 321 w 33906 I 19328 O 14 L 31.52 31.63 31.62
@#@FSLOADPOST 2020:07:15:18:43:33 longmc N 5 31.55 31.64 31.63
Linux c5-31 3.10.0-957.12.2.el7.x86_64 #1 SMP Tue May 14 21:24:32 UTC
2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 007_Run1.long.007_Run1_base exited with ERRORS at Wed
Jul 15 18:43:33 CEST 2020

Knut J?rgen Bjuland

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