[Freesurfer] Raw Data for Clusters

[WON JONG CHWA]

External Email - Use Caution

Dear FreeSurfer Experts,

I am running Qdec 1.4 and I want to extract raw data (in this case, volume)
from the significant clusters after Monte-Carlo simulation. In this
particular case, the summary file shows 5 significant clusters after
correction:

# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
# CreationTime 2018/10/16-23:28:21-GMT
# cmdline mri_surfcluster --in
/Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh
--csd
/Users/user/MyInstall/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm18/abs/th13/mc-z.csd
--mask /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/mask.mgh
--cwsig
/Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.mgh
--vwsig
/Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.vertex.mgh
--sum
/Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.cluster.summary
--ocn
/Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.mgh
--oannot
/Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.sig.ocn.annot
--csdpdf
/Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.pdf.dat
--annot aparc --cwpvalthresh 0.05 --o
/Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/mc-z.abs.th13.masked.mgh
--surf white
# cwd /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only
# sysname  Darwin
# hostname N-Volunteer-iMac.local
# machine  x86_64
# FixVertexAreaFlag 1
# FixSurfClusterArea 1
#
# Input
/Volumes/TRIALS/SCZ/TRIAL3.5_Males_only/qdec/Verification1/rh-Diff-SZ-HC-Intercept-volume/sig.mgh
# Frame Number  0
# srcsubj fsaverage
# hemi rh
# surface white
# annot aparc
# SUBJECTS_DIR /Volumes/TRIALS/SCZ/TRIAL3.5_Males_only
# SearchSpace_mm2 64328
# SearchSpace_vtx 149926
# Bonferroni 0
# Minimum Threshold 1.3
# Maximum Threshold infinity
# Threshold Signabs
# AdjustThreshWhenOneTail 1
# CW PValue Threshold: 0.05
# Area Threshold0 mm^2
# CSD thresh  1.30
# CSD nreps1
# CSD simtype  null-z
# CSD contrast NA
# CSD confint  90.00
# Overall max 2.06685 at vertex 34785
# Overall min -4.82491 at vertex 356
# NClusters  5
# Total Cortical Surface Area 64328 (mm^2)
# FixMNI = 1
#
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWP
CWPLowCWPHi   NVtxs   Annot
   1   -4.825 356   2272.51 60.8   -9.4   -1.7  0.00010
0.0  0.00020  3745  superiortemporal
   2   -4.419  146292   2658.98 19.8   52.0   -5.7  0.00010
0.0  0.00020  3104  rostralmiddlefrontal
   3   -4.267  138330   1525.99 35.6   35.27.0  0.00460
0.00370  0.00550  1936  rostralmiddlefrontal
   4   -3.304  140353   1712.65 34.9  -30.2   56.6  0.00220
0.00160  0.00280  3540  postcentral
   5   -3.050   28351   1096.87 19.6  -34.8   -8.7  0.04530
0.04260  0.04800  1687  parahippocampal

--
However, when I run the command to extract the raw data from these clusters
using this line:
mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf
mc-z.abs.th13.cluster.ocn.dat
--excludeid 0

The terminal window outputs this:

rh-Diff-SZ-HC-Intercept-volume user$ mri_segstats --i y.mgh --seg
mc-z.abs.th13.sig.cluster.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat
--excludeid 0



$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $

cwd

cmdline mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.cluster.mgh --avgwf
mc-z.abs.th13.cluster.ocn.dat --excludeid 0

sysname  Darwin

hostname N-Volunteer-iMac.local

machine  x86_64

user user

UseRobust  0

Loading mc-z.abs.th13.sig.cluster.mgh

Loading y.mgh

Voxel Volume is 1 mm^3

Generating list of segmentation ids

Found   4 segmentations

Computing statistics for each segmentation

  0-4   68496849.000

  1-2   54765476.000

  2-1   16871687.000



Reporting on   3 segmentations

Computing spatial average of each frame

  0  1  2

Writing to mc-z.abs.th13.cluster.ocn.dat

mri_segstats done
-

So I get a .dat file that only has 3 columns, which does not match up to
the 5 that I originally observed after the correction. If you could let me
know what the problem is that would be greatly appreciated.

Thank you.

William
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Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Ting Li]

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If I loaded the label to the inflated surface, it also gives me the cluster 
with branches. As you can see in the below. 

If I loaded the annot file to the inflated surface, it works well. Thanks for 
your help. 

Ting 



> On Oct 16, 2018, at 1:51 PM, Greve, Douglas N.,Ph.D.  
> wrote:
> 
> Hmm, not sure what to tell you. The label is derived directly from the 
> annot. If you click on a vertex in the branch, does it appear to be in 
> the label based on what displays in the control panel? If you load it on 
> the inflated surface, do you still see the branch?
> 
> On 10/15/2018 08:42 PM, Ting Li wrote:
>> External Email - Use Caution
>> 
>> The annot file loaded successfully and without any branches. Thanks a lot.
>> 
>> Ting
>>> On Oct 15, 2018, at 2:22 PM, Greve, Douglas N.,Ph.D. 
>>>  wrote:
>>> 
>>> Click on the surface file name in the upper left corner of FreeView,
>>> then load the Annotation from the panel just below it. It does not make
>>> sense that you would see the branches on the folded surface but not on
>>> the inflated.
>>> 
>>> On 10/15/2018 03:06 PM, Ting Li wrote:
 External Email - Use Caution
 
 I didn't load the annot file. I just use the annot file to create the
 label. if I check the clusters in a inflated brain, they are looks
 fine. If I need to load annot file for checking, how can I do it?
 Thanks a lot.
 
 Ting
 
 On Mon, Oct 15, 2018 at 9:25 AM Greve, Douglas N.,Ph.D.
 mailto:dgr...@mgh.harvard.edu>> wrote:
 
does the same thing happen when you load the annot file?
 
On 10/13/18 10:03 PM, Ting Li wrote:
>External Email - Use Caution
> 
>Dear Dr. Douglas,
> 
>I can load the label, but some clusters have branches. Some of
>them are just looks fine. Do you know the reason? Thanks a lot.
> 
>Regards,
>Ting
> 
> 
> 
> 
>>On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D.
>>mailto:dgr...@mgh.harvard.edu>> wrote:
>> 
>>yes, that is fine
>> 
>>On 10/11/18 11:21 PM, Ting Li wrote:
>>>External Email - Use Caution
>>> 
>>>Dear Dr. Douglas,
>>> 
>>>Thank you so much for your response. With your instruction, it
>>>works. This is how I did.
>>> 
>>>First, copy the significant cluster annot file from the
>>>simulation fold to one of subject label folder.
>>>Secondly, use the mir_annotation2label command to make this
>>>cluster into a label file
>>>Thirdly, copy this label file to fsaverage label folder
>>>Finally, I can load the label to the fsaverage surf.
>>> 
>>>Is this the right procedure? Thanks a lot!
>>> 
>>>Regards,
>>>Ting
On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>> wrote:
 
Which subject did you load it on? It must be fsaverage. Can
you send the
terminal output and command line?
 
On 10/03/2018 11:31 PM, Ting Li wrote:
>External Email - Use Caution
> 
>Dear Freesurfer Expert,
> 
>I have figured out the problem is that I didn’t specify lh
>before the
>annot file. However, in this method, I didn’t get the right
>label for
>I have loaded the label into the subject file. It is the
>scatter points.
> 
>I want to create label through mri_glm-fit-sim clusters. What
>command
>I should use? Please specify it for me. Thanks a lot!
> 
>Your help means a lot.
> 
>Regards,
>Ting
>>On Oct 3, 2018, at 9:38 PM, Ting Li >
>>> wrote:
>> 
>>I have also tried the command without annot in specifying the
>>annotation file. Thanks a lot.
>> 
>>Regards,
>> 
>>Ting
>>>On Oct 3, 2018, at 9:36 PM, Ting Li >>
>>>> wrote:
>>> 
>>>Dear Freesurfer Experts,
>>> 
>>>I really need your attention and help. Thanks a lot.
>>> 
>>>We want to create label through the mri_glm-fit-sim cluster
>>>results.
>>> 
>>>We have found the same topic in 2013 and tried the method
>>>you have
>>>provided. However, it doesn’t work. If you think it is not
>>>the right
>>>way, could you give me an example to do it right. I really
>>>appreciate your great help. Thanks a lot.
>>> 
>>>Here is my code:
>>> 

Re: [Freesurfer] FreeSurfer Errors (2)

[Sparsh Jain]

External Email - Use Caution

I attached that to the previous email, but it got rejected by the moderator
for some reason!

Sparsh

On Tue, Oct 16, 2018 at 1:03 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> can you send the command-line output as text?
>
> On 10/16/2018 11:12 AM, Sparsh Jain wrote:
> >
> > External Email - Use Caution
> >
> > Hey!
> > I sent two responses on Friday. The second response was bigger than 1
> > MB so it awaited moderator approval. I don't know if you received it
> > eventually.
> >
> > Following up to that mail, my reconstruction on the subject with 176
> > images crashed after about 32 hours of execution with the error 'could
> > not read label' and 'too many symbolic links' in fsaverage. I have
> > attached the entire command line output. Please help me understand
> > what I'm doing wrong !
> >
> > Thanks
> >
> > Sparsh
> >
> >
> >
> >
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Re: [Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

[Greve, Douglas N.,Ph.D.]

You can load them in freeview through tksurferfv, something like
tksurferfv fsaverage lh inflated -aparc -ov 
fmcpr.odd.sm5.fsaverage.lh.nii.gz
There's not much to see:)



On 10/16/2018 03:00 PM, Jacob Matthews wrote:
>
> External Email - Use Caution
>
> Hi FS Team,
>
> We are running our first fsfast pipeline, and starting with a single 
> subject to test everything. We successfully ran preproc-sess with the 
> following command:
>
> preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5 
> -per-run -sliceorder odd -fsd bold
>
> We wanted to check the outputs. It was clear how to view most 
> intermediate outputs, but we didn't know how to view the surface space 
> outputs:
> fmcpr.odd.sm5.fsaverage.rh.nii.gz
> fmcpr.odd.sm5.fsaverage.lh.nii.gz
>
> Loading them into freeview as surfaces fails. We thought perhaps they 
> needed to be loaded on top of an fsaverage surface, but didn't know 
> where to start this process.
>
> Thanks,
>
> Jacob Matthews
> MRI Specialist
> Rotman Research Institute
> Baycrest Hospital
> 416-785-2500 ext. 3322
>
>
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Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

[Greve, Douglas N.,Ph.D.]

which coords are you looking at? They should be the "surface RAS" coords.

On 10/16/2018 04:05 PM, Bruss, Joel E wrote:
>
> External Email - Use Caution
>
> I couldn't remember if it's 1+ or 1-.  Either way, either direction 
> give similar coordinates that don't match up to what I can see in 
> FreeView.
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Tuesday, October 16, 2018 1:48:14 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [External] Re: [Freesurfer] Nonsensical Vertex Coordinates, 
> please help with interpretation
> When you look at the vertex in matlab, are you correctly accounting for
> the fact that FreeView uses 0-based indexing and matlab uses 1-based?
> Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be
> using 234740 in matlab below
>
> On 10/15/2018 05:11 PM, Bruss, Joel E wrote:
> >
> > External Email - Use Caution
> >
> > I'm trying to make a surface file from a subject's head and to map
> > coordinates to that surface.  If I run:
> >
> >
> > mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol
> > $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2
> > 20 --nhitsmin 2
> >
> > mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255
> > $SUBJECTS_DIR/$sub/surf/lh.seghead
> >
> > and then load lh.seghead in FreeView, it looks as I would expect.
> > Clicking anywhere near a vertex gives the typical output, showing the
> > closest vertex.  All fine and well. However, if I load the file in 
> Matlab:
> >
> >
> > vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead');
> >
> >
> > my values are nothing near what I'm seeing in Freeview.  For example,
> > FreeView reports:
> >
> >
> > vertex 234741 [-78.50,14.50,26.50]
> >
> >
> > read_surf reports:
> >
> >
> > vertex 234740 0168.98000
> >
> > Of note, an error log tells me that:
> >
> > MRISreadNewCurvature: incompatible vertex number in file
> > $SUBJECTS_DIR/$sub/surf/lh.curv
> >
> >
> > How do I edit, update or create a curv file to play with the new
> > surface file, or what can I do to get sensical surface coordinates
> > from this data?
> >
> > Thanks,
> > Joel
> >
> >
> >
> >
> >
> >
> >
> >
> > 
> > Notice: This UI Health Care e-mail (including attachments) is covered
> > by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and
> > is intended only for the use of the individual or entity to which it
> > is addressed, and may contain information that is privileged,
> > confidential, and exempt from disclosure under applicable law. If you
> > are not the intended recipient, any dissemination, distribution or
> > copying of this communication is strictly prohibited. If you have
> > received this communication in error, please notify the sender
> > immediately and delete or destroy all copies of the original message
> > and attachments thereto. Email sent to or from UI Health Care may be
> > retained as required by law or regulation. Thank you.
> > 
> >
> >
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>
> 
> Notice: This UI Health Care e-mail (including attachments) is covered 
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Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

[Bruss, Joel E]

External Email - Use Caution

I couldn't remember if it's 1+ or 1-.  Either way, either direction give 
similar coordinates that don't match up to what I can see in FreeView.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Tuesday, October 16, 2018 1:48:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [External] Re: [Freesurfer] Nonsensical Vertex Coordinates, please 
help with interpretation

When you look at the vertex in matlab, are you correctly accounting for
the fact that FreeView uses 0-based indexing and matlab uses 1-based?
Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be
using 234740 in matlab below

On 10/15/2018 05:11 PM, Bruss, Joel E wrote:
>
> External Email - Use Caution
>
> I'm trying to make a surface file from a subject's head and to map
> coordinates to that surface.  If I run:
>
>
> mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol
> $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2
> 20 --nhitsmin 2
>
> mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255
> $SUBJECTS_DIR/$sub/surf/lh.seghead
>
> and then load lh.seghead in FreeView, it looks as I would expect.
> Clicking anywhere near a vertex gives the typical output, showing the
> closest vertex.  All fine and well. However, if I load the file in Matlab:
>
>
> vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead');
>
>
> my values are nothing near what I'm seeing in Freeview.  For example,
> FreeView reports:
>
>
> vertex 234741 [-78.50,14.50,26.50]
>
>
> read_surf reports:
>
>
> vertex 234740 0168.98000
>
> Of note, an error log tells me that:
>
> MRISreadNewCurvature: incompatible vertex number in file
> $SUBJECTS_DIR/$sub/surf/lh.curv
>
>
> How do I edit, update or create a curv file to play with the new
> surface file, or what can I do to get sensical surface coordinates
> from this data?
>
> Thanks,
> Joel
>
>
>
>
>
>
>
>
> 
> Notice: This UI Health Care e-mail (including attachments) is covered
> by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and
> is intended only for the use of the individual or entity to which it
> is addressed, and may contain information that is privileged,
> confidential, and exempt from disclosure under applicable law. If you
> are not the intended recipient, any dissemination, distribution or
> copying of this communication is strictly prohibited. If you have
> received this communication in error, please notify the sender
> immediately and delete or destroy all copies of the original message
> and attachments thereto. Email sent to or from UI Health Care may be
> retained as required by law or regulation. Thank you.
> 
>
>
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Notice: This UI Health Care e-mail (including attachments) is covered by the 
Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and is intended only 
for the use of the individual or entity to which it is addressed, and may 
contain information that is privileged, confidential, and exempt from 
disclosure under applicable law. If you are not the intended recipient, any 
dissemination, distribution or copying of this communication is strictly 
prohibited. If you have received this communication in error, please notify the 
sender immediately and delete or destroy all copies of the original message and 
attachments thereto. Email sent to or from UI Health Care may be retained as 
required by law or regulation. Thank you.

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Re: [Freesurfer] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution

There surely seems to be a link indeed; I'll look at where to correct the labeling and will give you feedback on the result. In the meantime, should you have any advice on such an optimal way, I'll be glad to hear it.

I'll keep you posted soon in all cases.

Many thanks for your help,
Maxime
​



De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Diamond, Bram Ryder 
Envoyé : 16 octobre 2018 14:54
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Possibly - I would definitely start there. The surfaces are following the
corpus callosum into the right hemisphere because the aseg labeling is off.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Maxime Perron 
Sent: Tuesday, October 16, 2018 2:48:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 




External Email - Use Caution

Hi Bram,

I modified the label of the lateral ventricules because they were mislabeled too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think that can fix the middle line?
​ 

Thanks,
Maxime




De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Diamond, Bram Ryder 
Envoyé : 16 octobre 2018 14:36
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


What did you edit in the
 aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Maxime Perron 
Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 



External Email - Use Caution

Sorry. Here are the good links : 


http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t


Maxime 


On Oct 16, 2018, at 2:22 PM, Maxime Perron  wrote:



External Email - Use Caution


Hi Bram,


No worries.


Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h


Thanks,
Maxime 




On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder  wrote:




Hi Maxime,


I'm having trouble finding your data - can you please use the filedrop instead?


https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,
Bram





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


External Email - Use Caution


Hi Bram, 


Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!

Many thanks,
Maxime​
​ 

De : freesurfer-boun...@nmr.mgh.harvard.edu
  de la part de Diamond, Bram Ryder 
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you after the weekend.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu
  on behalf of Maxime Perron 
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


    External Email - Use Caution

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline. 

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Maxime Perron 
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

    External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime 

[Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

[Jacob Matthews]

External Email - Use Caution

Hi FS Team,

We are running our first fsfast pipeline, and starting with a single
subject to test everything. We successfully ran preproc-sess with the
following command:

preproc-sess -s 11987_20180731 -surface fsaverage lhrh -mni305 -fwhm 5
-per-run -sliceorder odd -fsd bold

We wanted to check the outputs. It was clear how to view most intermediate
outputs, but we didn't know how to view the surface space outputs:
fmcpr.odd.sm5.fsaverage.rh.nii.gz
fmcpr.odd.sm5.fsaverage.lh.nii.gz

Loading them into freeview as surfaces fails. We thought perhaps they
needed to be loaded on top of an fsaverage surface, but didn't know where
to start this process.

Thanks,

Jacob Matthews
MRI Specialist
Rotman Research Institute
Baycrest Hospital
416-785-2500 ext. 3322
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Possibly - I would definitely start there. The surfaces are following the 
corpus callosum into the right hemisphere because the aseg labeling is off.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, October 16, 2018 2:48:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Hi Bram,

I modified the label of the lateral ventricules because they were mislabeled 
too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think 
that can fix the middle line?
​

Thanks,
Maxime



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Diamond, Bram Ryder 

Envoyé : 16 octobre 2018 14:36
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline


Hi Maxime,


What did you edit in the aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Sorry. Here are the good links :

http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t

Maxime

On Oct 16, 2018, at 2:22 PM, Maxime Perron 
mailto:maxime.perro...@ulaval.ca>> wrote:


External Email - Use Caution

Hi Bram,

No worries.

Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h

Thanks,
Maxime

On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:


Hi Maxime,

I'm having trouble finding your data - can you please use the filedrop instead?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Bram,

Thank you very much for the reply, I'm glad you'll have some time to look at 
the issue. Please don't hesitate to contact me should anything specific be 
needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline

Hi Maxime,

I'll take a look at your data and the issue you're having and get back to you 
after the weekend.

Best,
Bram

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the 

Re: [Freesurfer] qdec analysis with more than 2 covariates

[Greve, Douglas N.,Ph.D.]

That looks like the terminal output for qdec. You cannot use qdec with 
your design. If you have questions about the FSGD, I'll be happy to 
answer them.

On 10/16/2018 11:00 AM, vittal korann wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
> Thank you for your response.
> I tried the link which you sent yesterday. But got stuck while 
> creating qdec.fsgd file.
> Below i have pasted the terminal output after loading the data.
>
> 1  Left-Lateral-Ventricle  continuous 0
> 2  Left-Inf-Lat-Vent  continuous 0
> 3  Left-Cerebellum-White-Matter  continuous 0
> 4  Left-Cerebellum-Cortex  continuous 0
> 5  Left-Thalamus-Proper  continuous 0
> 6  Left-Caudate  continuous 0
> 7  Left-Putamen  continuous 0
> 8  Left-Pallidum  continuous 0
> 9  3rd-Ventricle  continuous 0
> 10  4th-Ventricle  continuous 0
> 11  Brain-Stem  continuous 0
> 12  Left-Hippocampus  continuous 0
> 13  Left-Amygdala  continuous 0
> 14  CSF  continuous 0
> 15  Left-Accumbens-area  continuous 0
> 16  Left-VentralDC  continuous 0
> 17  Left-vessel  continuous 0
> 18  Left-choroid-plexus  continuous 0
> 19  Right-Lateral-Ventricle  continuous 0
> 20  Right-Inf-Lat-Vent  continuous 0
> 21  Right-Cerebellum-White-Matter continuous 0
> 22  Right-Cerebellum-Cortex  continuous 0
> 23  Right-Thalamus-Proper  continuous 0
> 24  Right-Caudate  continuous 0
> 25  Right-Putamen  continuous 0
> 26  Right-Pallidum  continuous 0
> 27  Right-Hippocampus  continuous 0
> 28  Right-Amygdala  continuous 0
> 29  Right-Accumbens-area  continuous 0
> 30  Right-VentralDC  continuous 0
> 31  Right-vessel  continuous 0
> 32  Right-choroid-plexus  continuous 0
> 33  WM-hypointensities  continuous 0
> 34  Optic-Chiasm  continuous 0
> 35  CC_Posterior  continuous 0
> 36  CC_Mid_Posterior  continuous 0
> 37  CC_Central  continuous 0
> 38  CC_Mid_Anterior  continuous 0
> 39  CC_Anterior  continuous 0
> 40  diagnosis  discrete 2
>     1  Schizophrenia
>     2  Control
> 41  Age  continuous 0
> 42  Birthplace  discrete 3
>     1  Statutory
>     2  Census
>     3  Rural
> 43  Upbringingplace discrete 3
>     1  Statutory
>     2  Census
>     3  Rural
> 44  Livingplace  discrete 3
>     1  Statutory
>     2  Census
>     3  Rural
>                 Continuous Factors:  Mean:       StdDev:
>                 ---  -       ---
>              Left-Lateral-Ventricle 6784.459      3582.583
>                   Left-Inf-Lat-Vent  363.189       163.344
>        Left-Cerebellum-White-Matter  13393.085      2875.553
>              Left-Cerebellum-Cortex  50654.337      7634.479
>                Left-Thalamus-Proper 7044.259      1254.886
>                        Left-Caudate 3267.819       728.738
>                        Left-Putamen 5221.959       863.333
>                       Left-Pallidum 1961.781       357.087
>                       3rd-Ventricle 1068.711       447.579
>                       4th-Ventricle 1673.963       641.339
>                          Brain-Stem  18975.526      3907.934
>                    Left-Hippocampus 3852.407       684.810
>                       Left-Amygdala 1625.463       378.770
>                                 CSF  983.626       305.507
>                 Left-Accumbens-area  587.848       155.803
>                      Left-VentralDC 3977.841       673.114
>                         Left-vessel 28.378        21.035
>                 Left-choroid-plexus  558.441       330.333
>             Right-Lateral-Ventricle 6224.989      3745.143
>                  Right-Inf-Lat-Vent  440.070       168.625
>       Right-Cerebellum-White-Matter  13111.263      2744.138
>             Right-Cerebellum-Cortex  52495.385      7167.728
>               Right-Thalamus-Proper 6732.170      1748.668
>                       Right-Caudate 3305.363       949.074
>                       Right-Putamen 4908.819      1155.840
>                      Right-Pallidum 1774.204       489.167
>                   Right-Hippocampus 3766.470      1019.353
>                      Right-Amygdala 1686.874       437.019
>                Right-Accumbens-area  539.763       151.780
>                     Right-VentralDC 3818.130       666.970
>                        Right-vessel 23.344        16.649
>                Right-choroid-plexus  620.948       414.269
>                  WM-hypointensities 4434.148     10311.009
>                        Optic-Chiasm  198.937        65.369
>                        CC_Posterior  973.467       157.378
>                    CC_Mid_Posterior  637.400       597.617
>                          CC_Central  625.374       497.642
>                     CC_Mid_Anterior  681.052       419.940
>                         CC_Anterior  870.274       237.412
>                                 Age 31.963         7.019
>
> Number of subjects:   27
> Number of factors:    44 (4 discrete, 40 continuous)
> Number of classes:    54
> Number of regressors: 2214
> 
> Data table 

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

[Greve, Douglas N.,Ph.D.]

Hmm, not sure what to tell you. The label is derived directly from the 
annot. If you click on a vertex in the branch, does it appear to be in 
the label based on what displays in the control panel? If you load it on 
the inflated surface, do you still see the branch?

On 10/15/2018 08:42 PM, Ting Li wrote:
>  External Email - Use Caution
>
> The annot file loaded successfully and without any branches. Thanks a lot.
>
> Ting
>> On Oct 15, 2018, at 2:22 PM, Greve, Douglas N.,Ph.D. 
>>  wrote:
>>
>> Click on the surface file name in the upper left corner of FreeView,
>> then load the Annotation from the panel just below it. It does not make
>> sense that you would see the branches on the folded surface but not on
>> the inflated.
>>
>> On 10/15/2018 03:06 PM, Ting Li wrote:
>>>  External Email - Use Caution
>>>
>>> I didn't load the annot file. I just use the annot file to create the
>>> label. if I check the clusters in a inflated brain, they are looks
>>> fine. If I need to load annot file for checking, how can I do it?
>>> Thanks a lot.
>>>
>>> Ting
>>>
>>> On Mon, Oct 15, 2018 at 9:25 AM Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>
>>> does the same thing happen when you load the annot file?
>>>
>>> On 10/13/18 10:03 PM, Ting Li wrote:
 External Email - Use Caution

 Dear Dr. Douglas,

 I can load the label, but some clusters have branches. Some of
 them are just looks fine. Do you know the reason? Thanks a lot.

 Regards,
 Ting




> On Oct 12, 2018, at 10:35 AM, Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> yes, that is fine
>
> On 10/11/18 11:21 PM, Ting Li wrote:
>> External Email - Use Caution
>>
>> Dear Dr. Douglas,
>>
>> Thank you so much for your response. With your instruction, it
>> works. This is how I did.
>>
>> First, copy the significant cluster annot file from the
>> simulation fold to one of subject label folder.
>> Secondly, use the mir_annotation2label command to make this
>> cluster into a label file
>> Thirdly, copy this label file to fsaverage label folder
>> Finally, I can load the label to the fsaverage surf.
>>
>> Is this the right procedure? Thanks a lot!
>>
>> Regards,
>> Ting
>>> On Oct 10, 2018, at 1:30 PM, Greve, Douglas N.,Ph.D.
>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>
>>> Which subject did you load it on? It must be fsaverage. Can
>>> you send the
>>> terminal output and command line?
>>>
>>> On 10/03/2018 11:31 PM, Ting Li wrote:
 External Email - Use Caution

 Dear Freesurfer Expert,

 I have figured out the problem is that I didn’t specify lh
 before the
 annot file. However, in this method, I didn’t get the right
 label for
 I have loaded the label into the subject file. It is the
 scatter points.

 I want to create label through mri_glm-fit-sim clusters. What
 command
 I should use? Please specify it for me. Thanks a lot!

 Your help means a lot.

 Regards,
 Ting
> On Oct 3, 2018, at 9:38 PM, Ting Li  
> > wrote:
>
> I have also tried the command without annot in specifying the
> annotation file. Thanks a lot.
>
> Regards,
>
> Ting
>> On Oct 3, 2018, at 9:36 PM, Ting Li > 
>> > wrote:
>>
>> Dear Freesurfer Experts,
>>
>> I really need your attention and help. Thanks a lot.
>>
>> We want to create label through the mri_glm-fit-sim cluster
>> results.
>>
>> We have found the same topic in 2013 and tried the method
>> you have
>> provided. However, it doesn’t work. If you think it is not
>> the right
>> way, could you give me an example to do it right. I really
>> appreciate your great help. Thanks a lot.
>>
>> Here is my code:
>>
>> mri_annotation2label --subject F999  --hemi lh --annotation
>> cache.th20.neg.sig.ocn.annot --labelbase lh.test_label
>>
>> Here is my error information:
>> subject = F999
>> annotation = cache.th20.neg.sig.ocn.annot
>> hemi = lh
>> labelbase = lh.test_label
>> surface   = white
>>
>> Reading surface
>>  

Re: [Freesurfer] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution
Hi Bram,

I modified the label of the lateral ventricules because they were mislabeled too (Freesurfer_S043_test). I didn't change the label of the CC_*. Do you think that can fix the middle line?
​ 

Thanks,
Maxime




De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Diamond, Bram Ryder 
Envoyé : 16 octobre 2018 14:36
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


What did you edit in the
 aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu  on behalf of Maxime Perron 
Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 



External Email - Use Caution

Sorry. Here are the good links : 


http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t


Maxime 


On Oct 16, 2018, at 2:22 PM, Maxime Perron  wrote:



External Email - Use Caution


Hi Bram,


No worries.


Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h


Thanks,
Maxime 




On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder  wrote:




Hi Maxime,


I'm having trouble finding your data - can you please use the filedrop instead?


https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,
Bram





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


External Email - Use Caution


Hi Bram, 


Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!

Many thanks,
Maxime​
​ 

De : freesurfer-boun...@nmr.mgh.harvard.edu
  de la part de Diamond, Bram Ryder 
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you after the weekend.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu
  on behalf of Maxime Perron 
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


    External Email - Use Caution

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline. 

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Maxime Perron 
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

    External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the 

Re: [Freesurfer] Nonsensical Vertex Coordinates, please help with interpretation

[Greve, Douglas N.,Ph.D.]

When you look at the vertex in matlab, are you correctly accounting for 
the fact that FreeView uses 0-based indexing and matlab uses 1-based? 
Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be 
using 234740 in matlab below

On 10/15/2018 05:11 PM, Bruss, Joel E wrote:
>
> External Email - Use Caution
>
> I'm trying to make a surface file from a subject's head and to map 
> coordinates to that surface.  If I run:
>
>
> mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol 
> $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2 
> 20 --nhitsmin 2
>
> mri_tessellate $SUBJECTS_DIR/$sub/mri/seghead.mgz 255 
> $SUBJECTS_DIR/$sub/surf/lh.seghead
>
> and then load lh.seghead in FreeView, it looks as I would expect.  
> Clicking anywhere near a vertex gives the typical output, showing the 
> closest vertex.  All fine and well. However, if I load the file in Matlab:
>
>
> vCoord=read_surf('$SUBJECTS_DIR/$sub/surf/lh.seghead');
>
>
> my values are nothing near what I'm seeing in Freeview.  For example, 
> FreeView reports:
>
>
> vertex 234741 [-78.50,14.50,26.50]
>
>
> read_surf reports:
>
>
> vertex 234740 0168.98000
>
> Of note, an error log tells me that:
>
> MRISreadNewCurvature: incompatible vertex number in file 
> $SUBJECTS_DIR/$sub/surf/lh.curv
>
>
> How do I edit, update or create a curv file to play with the new 
> surface file, or what can I do to get sensical surface coordinates 
> from this data?
>
> Thanks,
> Joel
>
>
>
>
>
>
>
>
> 
> Notice: This UI Health Care e-mail (including attachments) is covered 
> by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521 and 
> is intended only for the use of the individual or entity to which it 
> is addressed, and may contain information that is privileged, 
> confidential, and exempt from disclosure under applicable law. If you 
> are not the intended recipient, any dissemination, distribution or 
> copying of this communication is strictly prohibited. If you have 
> received this communication in error, please notify the sender 
> immediately and delete or destroy all copies of the original message 
> and attachments thereto. Email sent to or from UI Health Care may be 
> retained as required by law or regulation. Thank you.
> 
>
>
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Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Hi Maxime,


What did you edit in the aseg? It looks like the CC_* have been mislabeled.


Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, October 16, 2018 2:23:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Sorry. Here are the good links :

http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t

Maxime

On Oct 16, 2018, at 2:22 PM, Maxime Perron 
mailto:maxime.perro...@ulaval.ca>> wrote:


External Email - Use Caution

Hi Bram,

No worries.

Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h

Thanks,
Maxime

On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>> wrote:


Hi Maxime,

I'm having trouble finding your data - can you please use the filedrop instead?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Bram


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Bram,

Thank you very much for the reply, I'm glad you'll have some time to look at 
the issue. Please don't hesitate to contact me should anything specific be 
needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Diamond, Bram Ryder 
mailto:brdiam...@mgh.harvard.edu>>
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline

Hi Maxime,

I'll take a look at your data and the issue you're having and get back to you 
after the weekend.

Best,
Bram

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 de la part de Maxime Perron 
mailto:maxime.perro...@ulaval.ca>>
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. 
>> Although parcelisation has changed, the midline has not changed. I launched 
>> several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you 
>> have an idea?
>>
>> Best,
>> Maxime
>>
>>> 

Re: [Freesurfer] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution
Sorry. Here are the good links : 


http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t


Maxime 


On Oct 16, 2018, at 2:22 PM, Maxime Perron  wrote:



External Email - Use Caution


Hi Bram,


No worries.


Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h


Thanks,
Maxime 




On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder  wrote:




Hi Maxime,


I'm having trouble finding your data - can you please use the filedrop instead?


https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,
Bram





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


External
 Email - Use Caution


Hi Bram, 


Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!

Many thanks,
Maxime​
​ 

De : freesurfer-boun...@nmr.mgh.harvard.edu
  de la part de Diamond, Bram Ryder 
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you after the weekend.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu
  on behalf of Maxime Perron 
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


    External Email - Use Caution

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline. 

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Maxime Perron 
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

    External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg,
 -cp, -wm), but it didn't work. Do you have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
    External Email - Use Caution
 Hello FreeSurfer Developers,

 I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that
 

Re: [Freesurfer] Correction Needed for the Midline

[Maxime Perron]

External Email - Use Caution
Hi Bram,


No worries.


Here is the link : http://gate.nmr.mgh.harvard.edu/filedrop2/?a=al9nxdabh5h


Thanks,
Maxime 




On Oct 16, 2018, at 1:11 PM, Diamond, Bram Ryder  wrote:




Hi Maxime,


I'm having trouble finding your data - can you please use the filedrop instead?


https://gate.nmr.mgh.harvard.edu/filedrop2/


Thanks,
Bram





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


External
 Email - Use Caution


Hi Bram, 


Thank you very much for the reply, I'm glad you'll have some time to look at the issue. Please don't hesitate to contact me should anything specific be needed. I'll be happy to contribute!

Many thanks,
Maxime​
​ 

De : freesurfer-boun...@nmr.mgh.harvard.edu
  de la part de Diamond, Bram Ryder 
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
 



Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you after the weekend.


Best,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu
  on behalf of Maxime Perron 
Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
 


    External Email - Use Caution

Hi Freesurfer Experts,
 
About 2 weeks ago, I sent a question about the midline correction but have not yet received a feedback. I am wondering if someone had time to check my data or has an idea on how to correct the bad midline. 

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with different autorecon (wm, cp, noaseg); still, although the segmentation changes, the midline doesn’t follow the new segmentation.
 
Since 10 of my subjects show this error, a solution is much needed.
 
Many thanks for your help!
 
Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu  de la part de Maxime Perron 
Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

    External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, you will find a file named Freesurfer_S043_test in which I made modifications on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we will take a look. Please include voxel coordinates of the spots you think are inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. Although parcelisation has changed, the midline has not changed. I launched several types of autorecon (-noaseg,
 -cp, -wm), but it didn't work. Do you have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
    External Email - Use Caution
 Hello FreeSurfer Developers,

 I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found midline cutting error, that
 is the midline does not go through exactly the center of the brain in coronal cut. For example, the
 midline is a little bit fuzzy and goes through an hemisphere than the other (see attachment). I've
 searched in the mail list and ​I don't find the way to fix it. Does anyone have any idea to fix 

[Freesurfer] updateing freesurfer.

[Aaron Tanenbaum]

External Email - Use Caution

I tried updating freesurfer 6.0 using the command fs_update. I get the
following output.



>  Build is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
>Running this will update some of your freesurfer binaries.
>
>  Shall I proceed? [y/n/Abort]: y
>
> rsync -zbrlv --progress --suffix=.1539713469_bak rsync://
> surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c/*
> /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_6_0/
> receiving incremental file list
> rsync: change_dir
> "/dist/freesurfer/patches/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c"
> (in pub) failed: No such file or directory (2)
>
> sent 8 bytes  received 173 bytes  362.00 bytes/sec
> total size is 0  speedup is 0.00
> rsync error: some files/attrs were not transferred (see previous errors)
> (code 23) at main.c(1655) [Receiver=3.1.1]
>
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[Freesurfer] Adding longitudinal time points to clean dataset {Disarmed}

[Molly Prigge]

External Email - Use Caution

Hello Freesurfer experts,

We have a large longitudinal dataset (n=~200) of up to 4 time points per 
participant.  All images were processed using Freesurfer v6.0 and have already 
undergone QA, and editing the cross, Base or long where needed.

We are finishing up collection of a 5th time point and will begin collecting a 
6th time point next year (average interscan interval 2.5 years).  We are 
running the new scans through the same Freesurfer v6.0 and same workstation as 
the previous time points.

Is it appropriate to use the Bases already created with Times 1-4 for the 5th 
and 6th timepoint long file creation?  We are hoping to avoid losing all the QA 
editing already done on the Base and long files from Times 1-4 and not have to 
redo all QA on Times 1-5 long files when time 6 is complete.

We appreciate any guidance.

Thanks!
Molly

---
Molly DuBray Prigge, PhD
Research Associate
Department of Pediatrics
molly.prigge at hsc.utah.edu
MRI Study Phone: 801.585.9061

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Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

[Bruce Fischl]

Hi Amanda

can you try it in freeview? tksurfer has been deprecated for a while now

cheers
Bruce
On 
Tue, 16 Oct 2018, Worker, Amanda wrote:




External Email - Use Caution

Thank you!


So the answer to the first question is that yes I can convert it back to a
curvature file and that curvature file can be loaded as an overlay. So this
must mean that the problem is with reading the .asc file rather than the
file being corrupt?


Cheers,


Amanda


From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Bruce Fischl

Sent: 15 October 2018 17:06:26
To: Freesurfer support list
Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
 
Hi Amanda

mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz

should do the trick
cheers
Bruce
On Mon, 15 Oct
2018, Worker, Amanda wrote:

>
> External Email - Use Caution
>
> How would I do that? mris_convert doesn't seem to take .asc as an input?
>
>
>
>___
_
> From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of
> Greve, Douglas N.,Ph.D. 
> Sent: 15 October 2018 16:25:51
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Using a .asc file as overlay in
freeview/tksurfer  
> Not sure. Can you use mris_convert to convert the asc back to a curv file?
>
> On 10/15/2018 11:20 AM, Worker, Amanda wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> >
> > I am trying to overlay a .asc file in either freeview or tksurfer, but
> > so far having no luck.
> >
> >
> > As practice and to determine the right format, I am simply using
> > lh.thickness, which I've converted to .asc using the following command:
> >
> >
> > % mris_convert -c lh.thickness lh.white lh.thickness.asc
> >
> >
> > I am trying to overlay this onto lh.pial for one subject, however I
> > cannot load the file and I get the following error message:
> >
> >
> > % mri_read(): couldn't determine type of file
>>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
62a631d19/surf/lh.thickne
> ss.asc
> > surfer: couldn't load
>>/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c70
62a631d19/surf/lh.thickne
> ss.asc.
> >  If you were trying to load a functional volume, make sure
> > you selected the right registration method, and if necessary,
> > that the registration file exists.
> > If you were trying to load a volume-encoded value file,
> > make sure it has the same number of values as this surface
> > does vertices (128970).
> > sclv_read_from_volume: error in FunD_New
> >
> > Interestingly, I can load the file as a curvature file, but then can't
> > play around with the threshold.
> >
> >
> > Do you have any idea what I'm doing wrong? Any help would be
appreciated!
> >
> >
> > Thanks,
> >
> >
> > Amanda
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
>>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm
r.mgh.harvard.edu%2Fmailm
>an%2Flistinfo%2Ffreesurferdata=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3
ac3c35e85fb46f47e2c08d63
>2b28e63%7C8370cf1416f34c16b83c724071654356%7C0sdata=p6poNQ0vBOYwWAjR4U
jk5lfKTtIcbEDR6icoWCJ2mz
> 8%3Dreserved=0
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr
.mgh.harvard.edu%2Fmailm
>an%2Flistinfo%2Ffreesurferdata=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3
ac3c35e85fb46f47e2c08d63
>2b28e63%7C8370cf1416f34c16b83c724071654356%7C0sdata=p6poNQ0vBOYwWAjR4U
jk5lfKTtIcbEDR6icoWCJ2mz
> 8%3Dreserved=0
>
>

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Re: [Freesurfer] Correction Needed for the Midline

[Diamond, Bram Ryder]

Hi Maxime,

I'm having trouble finding your data - can you please use the filedrop instead?

https://gate.nmr.mgh.harvard.edu/filedrop2/

Thanks,
Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline


External Email - Use Caution

Hi Bram,

Thank you very much for the reply, I'm glad you'll have some time to look at 
the issue. Please don't hesitate to contact me should anything specific be 
needed. I'll be happy to contribute!

Many thanks,
Maxime​
​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Diamond, Bram Ryder 

Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline


Hi Maxime,


I'll take a look at your data and the issue you're having and get back to you 
after the weekend.


Best,

Bram


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Maxime Perron 

Sent: Tuesday, September 25, 2018 1:14:08 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline

External Email - Use Caution

Hi Freesurfer Experts,

About 2 weeks ago, I sent a question about the midline correction but have not 
yet received a feedback. I am wondering if someone had time to check my data or 
has an idea on how to correct the bad midline.

I tried to correct the aseg.presurf.mgz (Freesurfer v.6.0.0) many times with 
different autorecon (wm, cp, noaseg); still, although the segmentation changes, 
the midline doesn’t follow the new segmentation.

Since 10 of my subjects show this error, a solution is much needed.

Many thanks for your help!

Best,
Maxime​

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Maxime Perron 

Envoyé : 17 septembre 2018 10:00
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

External Email - Use Caution

Hi Freesurfer Experts,

I was wondering if you have had time to look at my data to correct my midline 
problems? Many of my subjects have this problem.

Best regards,
Maxime

De : Maxime Perron
Envoyé : 13 septembre 2018 22:29
À : Freesurfer support list
Objet : Re: [Freesurfer] Midline errors

Hi Bruce,

I upload my subject to the ftp site as you requested. In the file midline_MP, 
you will find a file named Freesurfer_S043_test in which I made modifications 
on the aseg.presurf. The other file is the participant without modification.

The problem of the midline is from the coronal slice 137 to 157. For example, 
Talairach: 1.9 4.6 14.3.

Thank you for all your help,
Maxime

> On Sep 13, 2018, at 10:08 AM, Bruce Fischl  wrote:
>
> Hi Maxime
>
> if you upload a gzipped tar file of the entire subject dir to our ftp site we 
> will take a look. Please include voxel coordinates of the spots you think are 
> inaccurate.
>
> cheers
> Bruce
> On Thu, 13 Sep 2018, Maxime Perron wrote:
>
>>   External Email - Use Caution
>>
>> Hi Freesurfer Experts,
>>
>> I tried to correct the midline with the information you provided me. Indeed, 
>> I tried to correct the aseg.presurf (Freesurfer v.6) using Freeview. 
>> Although parcelisation has changed, the midline has not changed. I launched 
>> several types of autorecon (-noaseg, -cp, -wm), but it didn't work. Do you 
>> have an idea?
>>
>> Best,
>> Maxime
>>
>>> On Aug 10, 2018, at 5:09 PM, Bruce Fischl  
>>> wrote:
>>>
>>> HI Maxime
>>>
>>> check the aseg labels and make sure they are correct (and fix them if not). 
>>> Probably a couple of left/right ventricle voxels are mislabeled
>>> Bruce
>>> On Fri, 10 Aug 2018, Maxime Perron wrote:
>>>
External Email - Use Caution
 Hello FreeSurfer Developers,

 I use Freesurfer 6 on macOS Sierra 10.12.6. In several subjects, I found 
 midline cutting error, that
 is the midline does not go through exactly the center of the brain in 
 coronal cut. For example, the
 midline is a little bit fuzzy and goes through an hemisphere than the 
 other (see attachment). I've
 searched in the mail list and ​I don't find the way to fix it. Does anyone 
 have any idea to fix it?
 Thank you,
 Maxime Perron
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>>>
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>>> 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
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>>> error
>>> but does not contain patient information, 

Re: [Freesurfer] FreeSurfer Errors (2)

[Greve, Douglas N.,Ph.D.]

can you send the command-line output as text?

On 10/16/2018 11:12 AM, Sparsh Jain wrote:
>
> External Email - Use Caution
>
> Hey!
> I sent two responses on Friday. The second response was bigger than 1 
> MB so it awaited moderator approval. I don't know if you received it 
> eventually.
>
> Following up to that mail, my reconstruction on the subject with 176 
> images crashed after about 32 hours of execution with the error 'could 
> not read label' and 'too many symbolic links' in fsaverage. I have 
> attached the entire command line output. Please help me understand 
> what I'm doing wrong !
>
> Thanks
>
> Sparsh
>
>
>
>
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Re: [Freesurfer] Longitudinal stream : LME and limits of model

[Matthieu Vanhoutte]

External Email - Use Caution

Hi Martin,

It's been a long time since this discussion but I return on this from
now... The problem is that I followed longitudinal images of two groups
where I had mainly missing time points at the end. Than you suggested:
*If you have mainly missing time points at the end, this will bias your
analysis to some extend, as the remaining ones may be extremely healthy, as
probably the more diseased ones drop out. You may want to do a
time-to-event (or survival-analysis) which considers early drop-out.*

1) I know the survival analysis toolbox on matlab, but now I would like to
know what information will this survival analysis give to me ?
2) Will this analysis tell me if there is a bias ?
3) How to consider early drop-out with this type of analysis based on
mass-univariate LME analysis of longitudinal neuroimaging data ?

Thanks in advance for helping.

Best,
Matthieu

Le mer. 14 déc. 2016 à 22:14, Martin Reuter  a
écrit :

> Hi Matthieu,
>
> 1. yes, LME needs to be done first so that values can be sampled from the
> fitted model for the SA.
>
> 2. yes, I was talking about gradient non-linearities etc that could be in
> the image from the acquisition. We currently don’t use non-linear
> registration across time points (only rigid).
>
> Best, Martin
>
>
> On Nov 22, 2016, at 9:31 PM, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> wrote:
>
> Hi Martin,
>
> Please see inline below:
>
> Le 22 nov. 2016 à 17:04, Martin Reuter  a
> écrit :
>
> Hi Matthieu,
> (also inline)
>
> On Nov 21, 2016, at 10:28 PM, Matthieu Vanhoutte <
> matthieuvanhou...@gmail.com> wrote:
>
> Hi Martin,
>
> Thanks for replying. Please see inline below:
>
> Le 21 nov. 2016 à 20:26, Martin Reuter  a
> écrit :
>
> Hi Matthieu,
>
> a few quick answers. Maybe Jorge knows more.
> Generally number of subjects / time points etc. cannot be specified
> generally. All depends on how noisy your data is and how large the effect
> is that you expect to detect. You can do a power analysis in order to
> figure out how many subject / time points would be needed. There are some
> tools for that in the LME toolbox:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#Poweranalysis
>
>
> 1. see above
> 2. yes, also time points can miss from the middle. If you have mainly
> missing time points at the end, this will bias your analysis to some
> extend, as the remaining ones may be extremely healthy, as probably the
> more diseased ones drop out. You may want to do a time-to-event (or
> survival-analysis) which considers early drop-out.
>
>
> Is there any way to do with Freesurfer this kind of analysis ?
>
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/SurvivalAnalysis
> Yes, there is also a paper where we do this. It is a combination of LME
> and Survival Analysis (as for the SA you need to have measurements of all
> subjects at all time points, so you estimate that from the LME model).
>
>
> Thank you for the link, I will take a look at. So if understand, this
> analysis has to be done after LME statistical analysis ? Thereafter since
> SA need all time points, LME model will allow me to estimate missing time
> points ?
>
>
>
> 3. see above (power analysis)
> 4. GIGO means garbage in, garbage out, so the less you QC, the more likely
> will your results be junk. The more you QC the less likely will it be junk,
> but could still be. The FS wiki has lots of tutorial information on
> checking freesurfer recons. For longitudinal, you should additionally check
> the surfaces in the base, the brain mask in the base, and the alignment of
> the time points (although there is some wiggle space for the alignment, as
> most things are allowed to evolve further for each time point).
>
>
> For the alignment of the time points, should I better comparing brainmask
> or norm.mgz ?
>
>
> It does not really matter, I would use norm.mgz. I would load images on
> top of each other and then use the opacity slider in Freeview to blend
> between them (that way the eye can pick up small motions). I would not
> worry too much about local deformations which could be caused by
> non-linearity (gradient). But if you see global misalignment (rotation,
> translation) it is a cause for concern) .
>
>
> Ok thank you. The non-linearity you are talking about are well provoked by
> MRI system and not non-linear registration between time points and template
> base, aren’t they ?
>
> Best regards,
> Matthieu
>
>
>
> In order to avoid bias by adding further time points in the model by the
> -add recon all command, is this better for each subject to take into
> account all the time points existing for it or only the ones that I will
> include in the model (three time points / subject ; if existing 6 time
> points for any subject ?)
>
>
> Usually it is recommended to run all time points in the model (so a base
> with 6 time points) and not use the - - add flag. Also, Linear Mixed
> Effects models deal well with missing time points. 

Re: [Freesurfer] qdec analysis with more than 2 covariates

[vittal korann]

External Email - Use Caution

Hi Doug,

Thank you for your response.
I tried the link which you sent yesterday. But got stuck while creating
qdec.fsgd file.
Below i have pasted the terminal output after loading the data.

1  Left-Lateral-Ventricle  continuous 0
2  Left-Inf-Lat-Vent  continuous 0
3  Left-Cerebellum-White-Matter  continuous 0
4  Left-Cerebellum-Cortex  continuous 0
5  Left-Thalamus-Proper  continuous 0
6  Left-Caudate  continuous 0
7  Left-Putamen  continuous 0
8  Left-Pallidum  continuous 0
9  3rd-Ventricle  continuous 0
10  4th-Ventricle  continuous 0
11  Brain-Stem  continuous 0
12  Left-Hippocampus  continuous 0
13  Left-Amygdala  continuous 0
14  CSF  continuous 0
15  Left-Accumbens-area  continuous 0
16  Left-VentralDC  continuous 0
17  Left-vessel  continuous 0
18  Left-choroid-plexus  continuous 0
19  Right-Lateral-Ventricle  continuous 0
20  Right-Inf-Lat-Vent  continuous 0
21  Right-Cerebellum-White-Matter  continuous 0
22  Right-Cerebellum-Cortex  continuous 0
23  Right-Thalamus-Proper  continuous 0
24  Right-Caudate  continuous 0
25  Right-Putamen  continuous 0
26  Right-Pallidum  continuous 0
27  Right-Hippocampus  continuous 0
28  Right-Amygdala  continuous 0
29  Right-Accumbens-area  continuous 0
30  Right-VentralDC  continuous 0
31  Right-vessel  continuous 0
32  Right-choroid-plexus  continuous 0
33  WM-hypointensities  continuous 0
34  Optic-Chiasm  continuous 0
35  CC_Posterior  continuous 0
36  CC_Mid_Posterior  continuous 0
37  CC_Central  continuous 0
38  CC_Mid_Anterior  continuous 0
39  CC_Anterior  continuous 0
40  diagnosis  discrete 2
1  Schizophrenia
2  Control
41  Age  continuous 0
42  Birthplace  discrete 3
1  Statutory
2  Census
3  Rural
43  Upbringingplace  discrete 3
1  Statutory
2  Census
3  Rural
44  Livingplace  discrete 3
1  Statutory
2  Census
3  Rural
Continuous Factors: Mean:   StdDev:
--- -   ---
 Left-Lateral-Ventricle  6784.459  3582.583
  Left-Inf-Lat-Vent   363.189   163.344
   Left-Cerebellum-White-Matter 13393.085  2875.553
 Left-Cerebellum-Cortex 50654.337  7634.479
   Left-Thalamus-Proper  7044.259  1254.886
   Left-Caudate  3267.819   728.738
   Left-Putamen  5221.959   863.333
  Left-Pallidum  1961.781   357.087
  3rd-Ventricle  1068.711   447.579
  4th-Ventricle  1673.963   641.339
 Brain-Stem 18975.526  3907.934
   Left-Hippocampus  3852.407   684.810
  Left-Amygdala  1625.463   378.770
CSF   983.626   305.507
Left-Accumbens-area   587.848   155.803
 Left-VentralDC  3977.841   673.114
Left-vessel28.37821.035
Left-choroid-plexus   558.441   330.333
Right-Lateral-Ventricle  6224.989  3745.143
 Right-Inf-Lat-Vent   440.070   168.625
  Right-Cerebellum-White-Matter 13111.263  2744.138
Right-Cerebellum-Cortex 52495.385  7167.728
  Right-Thalamus-Proper  6732.170  1748.668
  Right-Caudate  3305.363   949.074
  Right-Putamen  4908.819  1155.840
 Right-Pallidum  1774.204   489.167
  Right-Hippocampus  3766.470  1019.353
 Right-Amygdala  1686.874   437.019
   Right-Accumbens-area   539.763   151.780
Right-VentralDC  3818.130   666.970
   Right-vessel23.34416.649
   Right-choroid-plexus   620.948   414.269
 WM-hypointensities  4434.148 10311.009
   Optic-Chiasm   198.93765.369
   CC_Posterior   973.467   157.378
   CC_Mid_Posterior   637.400   597.617
 CC_Central   625.374   497.642
CC_Mid_Anterior   681.052   419.940
CC_Anterior   870.274   237.412
Age31.963 7.019

Number of subjects:   27
Number of factors:44 (4 discrete, 40 continuous)
Number of classes:54
Number of regressors: 2214

Data table loading completed successfully.
SUBJECTS_DIR is '/usr/local/freesurfer/subjects'
lh-Avg-Intercept-thickness ---
Does the average thickness differ from zero?
Nuisance factors: Age
 1.000   

[Freesurfer] Postdoctoral positions available

[Chinappen, Dhinakaran Maheswaran]

Three, NIH-supported postdoctoral positions in computational neuroscience are 
available
immediately at Boston University in the labs of Uri Eden and Mark Kramer. The 
positions
center on two projects:

Project: Measure, model, and modulate cross-frequency coupling.
Team: An interdisciplinary team of researchers at BU (Mark Kramer and Uri Eden) 
and the
University of Minnesota (Alik Widge).
Goals: (i) Develop new statistical modeling methods to assess cross-frequency 
coupling
(CFC) in real-time, and deploy these tools in in vivo animal experiments. (ii) 
Develop simple,
biophysical models to identify candidate mechanisms of CFC.

Project: Assess human seizure dynamics across spatial and temporal scales.
Team: An interdisciplinary team of researchers at BU (Mark Kramer and Uri Eden)
Harvard/MGH (Sydney Cash), and Columbia University (Catherine Schevon).
Goals: (i) Analyze human seizure activity in a unique data set, consisting of 
invasive brain
voltage recordings across spatial scales - from single units to large brain 
areas, and temporal
scales - from high-frequency oscillations to slow brain rhythms. (ii) Build 
biophysical models to
probe how human seizures start, propagate, and stop.

For either project, the successful candidate will have a strong background in 
statistics
and computer programming; experience in interdisciplinary neuroscience research 
and
biophysical modeling is preferred, although not essential.

The positions are based at Boston University in the labs of Uri Eden and Mark 
Kramer. Both
projects are highly interdisciplinary and will involve frequent and extensive 
interactions with
neuroscientists at UMN (Alik Widge), or clinicians at Harvard/MGH (Sydney Cash) 
and
Columbia University (Catherine Schevon).

To apply, or for more information about the position, please send an email to 
Mark Kramer
(m...@math.bu.edu). Please include an updated CV, names and contact information 
of three
references, and a brief statement of your interest in the position and relevant 
qualifications.
Boston University offers a vibrant community of statistical, mathematical, and 
neuroscience
faculty and students, and many opportunities for collaboration within and 
outside the
University.



Dhinakaran M. Chinappen

Clinical Research Coordinator

Neurology Department

Massachusetts General Hospital

m: 1-267-257-1224
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[Freesurfer] Postdoctoral positions available

[Chu, Catherine,M.D.]

Multiple Postdoctoral Positions in Computational Neuroscience Available at 
Boston

University, and beyond.


Three, NIH-supported postdoctoral positions in computational neuroscience are 
available

immediately at Boston University in the labs of Uri Eden and Mark Kramer. The 
positions

center on two projects:


Project: Measure, model, and modulate cross-frequency coupling.

Team: An interdisciplinary team of researchers at BU (Mark Kramer and Uri Eden) 
and the

University of Minnesota (Alik Widge).

Goals: (i) Develop new statistical modeling methods to assess cross-frequency 
coupling

(CFC) in real-time, and deploy these tools in in vivo animal experiments. (ii) 
Develop simple,

biophysical models to identify candidate mechanisms of CFC.


Project: Assess human seizure dynamics across spatial and temporal scales.

Team: An interdisciplinary team of researchers at BU (Mark Kramer and Uri Eden)

Harvard/MGH (Sydney Cash), and Columbia University (Catherine Schevon).

Goals: (i) Analyze human seizure activity in a unique data set, consisting of 
invasive brain

voltage recordings across spatial scales - from single units to large brain 
areas, and temporal

scales - from high-frequency oscillations to slow brain rhythms. (ii) Build 
biophysical models to

probe how human seizures start, propagate, and stop.


For either project, the successful candidate will have a strong background in 
statistics

and computer programming; experience in interdisciplinary neuroscience research 
and

biophysical modeling is preferred, although not essential.


The positions are based at Boston University in the labs of Uri Eden and Mark 
Kramer. Both

projects are highly interdisciplinary and will involve frequent and extensive 
interactions with

neuroscientists at UMN (Alik Widge), or clinicians at Harvard/MGH (Sydney Cash) 
and

Columbia University (Catherine Schevon).


To apply, or for more information about the position, please send an email to 
Mark Kramer

(m...@math.bu.edu). Please include an updated CV, names and contact information 
of three

references, and a brief statement of your interest in the position and relevant 
qualifications.

Boston University offers a vibrant community of statistical, mathematical, and 
neuroscience

faculty and students, and many opportunities for collaboration within and 
outside the

University.



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Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

[Worker, Amanda]

External Email - Use Caution

Thank you!


So the answer to the first question is that yes I can convert it back to a 
curvature file and that curvature file can be loaded as an overlay. So this 
must mean that the problem is with reading the .asc file rather than the file 
being corrupt?


Cheers,


Amanda


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: 15 October 2018 17:06:26
To: Freesurfer support list
Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

Hi Amanda

mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz

should do the trick
cheers
Bruce
On Mon, 15 Oct
2018, Worker, Amanda wrote:

>
> External Email - Use Caution
>
> How would I do that? mris_convert doesn't seem to take .asc as an input?
>
>
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of
> Greve, Douglas N.,Ph.D. 
> Sent: 15 October 2018 16:25:51
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer
> Not sure. Can you use mris_convert to convert the asc back to a curv file?
>
> On 10/15/2018 11:20 AM, Worker, Amanda wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> >
> > I am trying to overlay a .asc file in either freeview or tksurfer, but
> > so far having no luck.
> >
> >
> > As practice and to determine the right format, I am simply using
> > lh.thickness, which I've converted to .asc using the following command:
> >
> >
> > % mris_convert -c lh.thickness lh.white lh.thickness.asc
> >
> >
> > I am trying to overlay this onto lh.pial for one subject, however I
> > cannot load the file and I get the following error message:
> >
> >
> > % mri_read(): couldn't determine type of file
> >/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
> ss.asc
> > surfer: couldn't load
> >/data/project/biobank/normative_modelling/DATA/03129b39-45a0-4491-9fdf-c7062a631d19/surf/lh.thickne
> ss.asc.
> >  If you were trying to load a functional volume, make sure
> > you selected the right registration method, and if necessary,
> > that the registration file exists.
> > If you were trying to load a volume-encoded value file,
> > make sure it has the same number of values as this surface
> > does vertices (128970).
> > sclv_read_from_volume: error in FunD_New
> >
> > Interestingly, I can load the file as a curvature file, but then can't
> > play around with the threshold.
> >
> >
> > Do you have any idea what I'm doing wrong? Any help would be appreciated!
> >
> >
> > Thanks,
> >
> >
> > Amanda
> >
> >
> >
> > ___
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> an%2Flistinfo%2Ffreesurferdata=01%7C01%7Camanda.worker%40kcl.ac.uk%7C3ac3c35e85fb46f47e2c08d63
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>
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