[Freesurfer] funcroi-table-sess error

[Alexandra Tanner]

Dear Doug and Freesurfers,

I am attempting to run funcroi-table-sess on a set of subjects but keep
getting an error message I've never seen before:

funcroi-table-sess -roi
/cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg
-sf
/cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED
-c Cond2vFix -o
/cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/18ActiveFolate_12Placebo_PreAndPost_7Tpost/ctx_lh_insula_aparc+aseg_2vFix


log/funcroi-table-sess.log
log/funcroi-table-sess.log: No such file or directory.


Funcroi-sess ran without error, as did funcroi-config. I've run this
analysis many times in the past and have never had this problem so I am at
a loss as to what is going wrong. Any help would be greatly appreciated!

Thanks,
Alex



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[Freesurfer] Funcroi-Table-Sess Error

[Morenikeji Adebayo]

Hi there,

I ran the following analysis commands:

mri_cor2label --c 
/autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 11106 
--l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh -roi 
roiconfig_ACC_lh
funcroi-table-sess -analysis analysis_induc_block.lh -contrast 
contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o 
sumtable_ACC_lh.dat

After running the 'funcroi-table-sess’ command I got the following error:

ERROR: There is a vertex in the label that cannot be matched to the surface. 
This usually occurs when the label and surface are from different subjects or 
hemispheres of the surface has been changed since the label was created.

It seems that the problem might be that the command is using my participant (in 
this case, nmasa_001) as the source subject  BUT it’s using fsaverage as the 
target subject. I want the target subject to be my participant as well (not 
fsaverage).

Is there a way that I can specify the target subjects? Or is there a more 
efficient way do what I’m trying to do (ie: 1. generate labels for each 
participant based on their aparc+aseg file and 2. calculate the mean contrast 
signal from each ROI for each participant).


Thanks,
Keji



---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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Re: [Freesurfer] funcroi-table-sess error

[Douglas Greve]

Hi Alex, are you running it from the project folder? It is looking for a 
folder called "log" in the current directory. It should be creating this 
folder (bug). So, if you run it from the project folder, the log folder 
will be there. Or can create a log folder in your current directory 
(mkdir log)

doug

On 7/30/13 2:03 PM, Alexandra Tanner wrote:
> Dear Doug and Freesurfers,
>
> I am attempting to run funcroi-table-sess on a set of subjects but keep
> getting an error message I've never seen before:
>
> funcroi-table-sess -roi
> /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg
> -sf
> /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED
> -c Cond2vFix -o
> /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/18ActiveFolate_12Placebo_PreAndPost_7Tpost/ctx_lh_insula_aparc+aseg_2vFix
>
>
> log/funcroi-table-sess.log
> log/funcroi-table-sess.log: No such file or directory.
>
>
> Funcroi-sess ran without error, as did funcroi-config. I've run this
> analysis many times in the past and have never had this problem so I am at
> a loss as to what is going wrong. Any help would be greatly appreciated!
>
> Thanks,
> Alex
>
>
>
>

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Re: [Freesurfer] funcroi-table-sess error

[Alexandra Tanner]

Hi Doug,

I was running the command out of the $SUBJECTS_DIR. I created a log folder
in the $SUBJECTS_DIR and then the command ran smoothly! Thanks!

Best,
Alex

>
> Hi Alex, are you running it from the project folder? It is looking for a
> folder called "log" in the current directory. It should be creating this
> folder (bug). So, if you run it from the project folder, the log folder
> will be there. Or can create a log folder in your current directory
> (mkdir log)
>
> doug
>
> On 7/30/13 2:03 PM, Alexandra Tanner wrote:
>> Dear Doug and Freesurfers,
>>
>> I am attempting to run funcroi-table-sess on a set of subjects but keep
>> getting an error message I've never seen before:
>>
>> funcroi-table-sess -roi
>> /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg
>> -sf
>> /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED
>> -c Cond2vFix -o
>> /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/18ActiveFolate_12Placebo_PreAndPost_7Tpost/ctx_lh_insula_aparc+aseg_2vFix
>>
>>
>> log/funcroi-table-sess.log
>> log/funcroi-table-sess.log: No such file or directory.
>>
>>
>> Funcroi-sess ran without error, as did funcroi-config. I've run this
>> analysis many times in the past and have never had this problem so I am
>> at
>> a loss as to what is going wrong. Any help would be greatly appreciated!
>>
>> Thanks,
>> Alex
>>
>>
>>
>>
>
>
>

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Re: [Freesurfer] Funcroi-Table-Sess Error

[Morenikeji Adebayo]

Hi there,

Just following up on this. Any help  would much appreciated!

Thanks,
Keji

> On Oct 23, 2015, at 1:46 PM, Morenikeji Adebayo  
> wrote:
> 
> Hi there,
> 
> I ran the following analysis commands:
> 
> mri_cor2label --c 
> /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 
> 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
> funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh 
> -roi roiconfig_ACC_lh
> funcroi-table-sess -analysis analysis_induc_block.lh -contrast 
> contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o 
> sumtable_ACC_lh.dat
> 
> After running the 'funcroi-table-sess’ command I got the following error:
> 
> ERROR: There is a vertex in the label that cannot be matched to the surface. 
> This usually occurs when the label and surface are from different subjects or 
> hemispheres of the surface has been changed since the label was created.
> 
> It seems that the problem might be that the command is using my participant 
> (in this case, nmasa_001) as the source subject  BUT it’s using fsaverage as 
> the target subject. I want the target subject to be my participant as well 
> (not fsaverage).
> 
> Is there a way that I can specify the target subjects? Or is there a more 
> efficient way do what I’m trying to do (ie: 1. generate labels for each 
> participant based on their aparc+aseg file and 2. calculate the mean contrast 
> signal from each ROI for each participant).
> 
> 
> Thanks,
> Keji
> 
> 
> 
> ---
> Morenikeji Adebayo
> Clinical Research Coordinator
> Department of Psychiatric Neuroscience
> Massachusetts General Hospital
> (p) 617.643.6347
> k...@nmr.mgh.harvard.edu 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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Re: [Freesurfer] Funcroi-Table-Sess Error

[Douglas Greve]

I think the problem is probably that you created the label from a volume 
whereas funcroi expects the label to come from a surface. Instead of 
using mri_cor2label and  -label for funcroi-config, try using something like


funcroi-config  -annot aparc.a2009s G_and_S_cingul-Ant -analysis 
analysis_induc_block.lh-roi roiconfig_ACC_lh

On 10/23/15 1:46 PM, Morenikeji Adebayo wrote:

Hi there,

I ran the following analysis commands:

 1. mri_cor2label --c
/autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id
11106 --l
/autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
 2. funcroi-config -labellabl_ACC_lh.label -analysis
analysis_induc_block.lh-roi roiconfig_ACC_lh
 3. funcroi-table-sess -analysis analysis_induc_block.lh -contrast
contrast_neg_V_neut -roi roiconfig_ACC_lh-sf
sublist_All_SHORT_n111 -o sumtable_ACC_lh.dat


After running the 'funcroi-table-sess’ command I got the following error:

ERROR: There is a vertex in the label that cannot be matched to
the surface. This usually occurs when the label and surface are
from different subjects or hemispheres of the surface has been
changed since the label was created.


It seems that the problem might be that the command is using my 
participant (in this case, nmasa_001) as the source subject  BUT it’s 
using fsaverage as the target subject. I want the target subject to be 
my participant as well (not fsaverage).


Is there a way that I can specify the target subjects? Or is there a 
more efficient way do what I’m trying to do (ie: 1. generate labels 
for each participant based on their aparc+aseg file and 2. calculate 
the mean contrast signal from each ROI for each participant).


Thanks,
Keji


--- Morenikeji Adebayo Clinical Research Coordinator Department of 
Psychiatric Neuroscience
Massachusetts General Hospital (p) 
617.643.6347k...@nmr.mgh.harvard.edu 


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Re: [Freesurfer] Funcroi-Table-Sess Error

[Morenikeji Adebayo]

Hi Doug,

Thanks for the help!  So, you’re saying that:

By specifying  a volume file (ie: aparc.a2009s+aseg.mgz) when using 
mri_cor2label, I’ve created volume labels
 The commands ‘funcroi-config' and 'funcroi-table-sess' accept only labels 
created on the surface.

Is this correct?

Thanks,
Keji


> On Oct 27, 2015, at 11:38 AM, Douglas Greve  wrote:
> 
> I think the problem is probably that you created the label from a volume 
> whereas funcroi expects the label to come from a surface. Instead of using 
> mri_cor2label and  -label for funcroi-config, try using something like
> 
> funcroi-config  -annot aparc.a2009s G_and_S_cingul-Ant  -analysis 
> analysis_induc_block.lh -roi roiconfig_ACC_lh
> 
> 
> 
> On 10/23/15 1:46 PM, Morenikeji Adebayo wrote:
>> Hi there,
>> 
>> I ran the following analysis commands:
>> 
>>  mri_cor2label --c 
>> /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 
>> 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
>> funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh 
>> -roi roiconfig_ACC_lh
>> funcroi-table-sess -analysis analysis_induc_block.lh -contrast 
>> contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o 
>> sumtable_ACC_lh.dat
>> 
>> After running the 'funcroi-table-sess’ command I got the following error:
>> 
>> ERROR: There is a vertex in the label that cannot be matched to the surface. 
>> This usually occurs when the label and surface are from different subjects 
>> or hemispheres of the surface has been changed since the label was created.
>> 
>> It seems that the problem might be that the command is using my participant 
>> (in this case, nmasa_001) as the source subject  BUT it’s using fsaverage as 
>> the target subject. I want the target subject to be my participant as well 
>> (not fsaverage).
>> 
>> Is there a way that I can specify the target subjects? Or is there a more 
>> efficient way do what I’m trying to do (ie: 1. generate labels for each 
>> participant based on their aparc+aseg file and 2. calculate the mean 
>> contrast signal from each ROI for each participant).
>> 
>> 
>> Thanks,
>> Keji
>> 
>> 
>> 
>> --- Morenikeji Adebayo Clinical Research Coordinator Department of 
>> Psychiatric Neuroscience
>> Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu 
>> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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Re: [Freesurfer] Funcroi-Table-Sess Error

[Douglas Greve]

On 10/27/15 1:09 PM, Morenikeji Adebayo wrote:

Hi Doug,

Thanks for the help!  So, you’re saying that:

 1. By specifying  a volume file (ie: aparc.a2009s+aseg.mgz) when
using mri_cor2label, I’ve created volume labels


Correct


 1. The commands ‘funcroi-config' and 'funcroi-table-sess' accept only
labels created on the surface.

It takes either. But the analysis you use is a surface-based analysis, 
so you need a surface-based label.

doug


Is this correct?
Thanks,
Keji

On Oct 27, 2015, at 11:38 AM, Douglas Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


I think the problem is probably that you created the label from a 
volume whereas funcroi expects the label to come from a surface. 
Instead of using mri_cor2label and  -label for funcroi-config, try 
using something like


funcroi-config  -annot aparc.a2009s G_and_S_cingul-Ant -analysis 
analysis_induc_block.lh-roi roiconfig_ACC_lh

On 10/23/15 1:46 PM, Morenikeji Adebayo wrote:

Hi there,

I ran the following analysis commands:

 1. mri_cor2label --c
/autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz
--id 11106 --l
/autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
 2. funcroi-config -labellabl_ACC_lh.label -analysis
analysis_induc_block.lh-roi roiconfig_ACC_lh
 3. funcroi-table-sess -analysis analysis_induc_block.lh -contrast
contrast_neg_V_neut -roi roiconfig_ACC_lh-sf
sublist_All_SHORT_n111 -o sumtable_ACC_lh.dat


After running the 'funcroi-table-sess’ command I got the following 
error:


ERROR: There is a vertex in the label that cannot be matched to
the surface. This usually occurs when the label and surface are
from different subjects or hemispheres of the surface has been
changed since the label was created.


It seems that the problem might be that the command is using my 
participant (in this case, nmasa_001) as the source subject  BUT 
it’s using fsaverage as the target subject. I want the target 
subject to be my participant as well (not fsaverage).


Is there a way that I can specify the target subjects? Or is there a 
more efficient way do what I’m trying to do (ie: 1. generate labels 
for each participant based on their aparc+aseg file and 2. calculate 
the mean contrast signal from each ROI for each participant).


Thanks,
Keji


--- Morenikeji Adebayo Clinical Research Coordinator Department of 
Psychiatric Neuroscience
Massachusetts General Hospital (p) 
617.643.6347k...@nmr.mgh.harvard.edu 


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Psychiatric Neuroscience
Massachusetts General Hospital (p) 
617.643.6347k...@nmr.mgh.harvard.edu 


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Re: [Freesurfer] Funcroi-Table-Sess Error

[Morenikeji Adebayo]

Thanks!!
> On Oct 27, 2015, at 1:18 PM, Douglas Greve  wrote:
> 
> 
> 
> On 10/27/15 1:09 PM, Morenikeji Adebayo wrote:
>> Hi Doug,
>> 
>> Thanks for the help!  So, you’re saying that:
>> 
>> By specifying  a volume file (ie: aparc.a2009s+aseg.mgz) when using 
>> mri_cor2label, I’ve created volume labels
> Correct
>>  The commands ‘funcroi-config' and 'funcroi-table-sess' accept only labels 
>> created on the surface.
> It takes either. But the analysis you use is a surface-based analysis, so you 
> need a surface-based label.
> doug
> 
>> 
>> Is this correct?
>> 
>> Thanks,
>> Keji
>> 
>> 
>>> On Oct 27, 2015, at 11:38 AM, Douglas Greve >> > wrote:
>>> 
>>> I think the problem is probably that you created the label from a volume 
>>> whereas funcroi expects the label to come from a surface. Instead of using 
>>> mri_cor2label and  -label for funcroi-config, try using something like
>>> 
>>> funcroi-config  -annot aparc.a2009s G_and_S_cingul-Ant  -analysis 
>>> analysis_induc_block.lh -roi roiconfig_ACC_lh
>>> 
>>> 
>>> 
>>> On 10/23/15 1:46 PM, Morenikeji Adebayo wrote:
 Hi there,
 
 I ran the following analysis commands:
 
 mri_cor2label --c 
 /autofs/cluster/iaslab/NMASA/mri/recon/$s/mri/aparc.a2009s+aseg.mgz --id 
 11106 --l /autofs/cluster/iaslab/NMASA/mri/recon/$s/label/labl_ACC_lh.label
 funcroi-config -label labl_ACC_lh.label -analysis analysis_induc_block.lh 
 -roi roiconfig_ACC_lh
 funcroi-table-sess -analysis analysis_induc_block.lh -contrast 
 contrast_neg_V_neut -roi roiconfig_ACC_lh -sf sublist_All_SHORT_n111 -o 
 sumtable_ACC_lh.dat
 
 After running the 'funcroi-table-sess’ command I got the following error:
 
 ERROR: There is a vertex in the label that cannot be matched to the 
 surface. This usually occurs when the label and surface are from different 
 subjects or hemispheres of the surface has been changed since the label 
 was created.
 
 It seems that the problem might be that the command is using my 
 participant (in this case, nmasa_001) as the source subject  BUT it’s 
 using fsaverage as the target subject. I want the target subject to be my 
 participant as well (not fsaverage).
 
 Is there a way that I can specify the target subjects? Or is there a more 
 efficient way do what I’m trying to do (ie: 1. generate labels for each 
 participant based on their aparc+aseg file and 2. calculate the mean 
 contrast signal from each ROI for each participant).
 
 
 Thanks,
 Keji
 
 
 
 --- Morenikeji Adebayo Clinical Research Coordinator Department of 
 Psychiatric Neuroscience
 Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu 
 
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 Freesurfer@nmr.mgh.harvard.edu 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
 ___
  Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  
>> --- Morenikeji Adebayo Clinical Research Coordinator Department of 
>> Psychiatric Neuroscience
>> Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu 
>> 
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> 
---
Morenikeji Adebayo
Clinical Research Coordinator
Department of Psychiatric Neuroscience
Massachusetts General Hospital
(p) 617.643.6347
k...@nmr.mgh.harvard.edu

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Re: [Freesurfer] funcroi-table-sess error, "variable must begin with a letter"

[Douglas N Greve]

The log file you sent has a different error:

ERROR: cannot find allVfix in NMASA_induction.lh


On 02/17/2015 01:40 PM, Joseph Andreano wrote:
> Hi Doug,
>
> We're having difficulty extracting signal from ROIs using
> funcroi-table-sess.  Every time we try, we get the following error
> message: "set: Variable name must begin with a letter."
>
> In an earlier discussion about this error
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39320.html)
> you asked for a debug version of the command we were having difficulty
> with.  The file is attached.
>
> Thanks,
> Joe Andreano
>
>
>
> _
>
> Joseph M. Andreano, PhD
> Postdoctoral Researcher
> Interdisciplinary Affective
> Science Laboratory
> Massachusetts General Hospital
> _
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] funcroi-table-sess error, \"set: Variable name must begin with a letter\"

[Morenikeji Adebayo]

Hi there,

I'm having the same problem referenced in this thread from last year. When I 
send the command:
funcroi-table-sess -roi l_ant_cingulate_allVfix.roicfg -analysis 
NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o 
l_ant_cingulate_induction_FIR_f0.dat -frame 0

I get the following error:
set: Variable name must begin with a letter.

I was wondering if there was any resolution to this issue when it came up last 
year or if you have any advice on how I should proceed now. I do have a folder 
named "log" in the directory I'm running the command from.

Thanks,
Keji
---
Morenikeji Adebayo
Clinical Research Coordinator
Interdisciplinary Affective Science Lab
Massachusetts General Hospital
Department of Psychiatric Neuroscience

(p) 617.643.6347
(f) 617.726.5760
k...@nmr.mgh.harvard.edu

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[Freesurfer] funcroi-table-sess error, "set: Variable name must begin with a letter"

[Joseph Andreano]

Hi All,

I'm trying to use funcroi-table-sess, but whenever I send this command:

funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305
-contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat

I get this error:

set: Variable name must begin with a letter

So far as I can tell, all the variables in that command begin with a 
letter.  Any idea what the problem might be?


_

Joseph M. Andreano, PhD
Postdoctoral Researcher
Interdisciplinary Affective
   Science Laboratory
Massachusetts General Hospital
_
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Re: [Freesurfer] funcroi-table-sess error, \"set: Variable name must begin with a letter\"

[Douglas N Greve]

I can't remember what the issue was. Can you run


funcroi-table-sess -debug -roi l_ant_cingulate_allVfix.roicfg -analysis 
NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o 
l_ant_cingulate_induction_FIR_f0.dat -frame 0 |& tee dng.log

and send me dng.log

doug

On 12/12/2014 03:03 PM, Morenikeji Adebayo wrote:
> Hi there,
>
> I'm having the same problem referenced in this thread from last year. 
> When I send the command:
> funcroi-table-sess -roi l_ant_cingulate_allVfix.roicfg -analysis 
> NMASA_induction.lh -contrast allVfix -sf induction_all2.lst -o 
> l_ant_cingulate_induction_FIR_f0.dat -frame 0
>
> I get the following error:
> set: Variable name must begin with a letter.
>
> I was wondering if there was any resolution to this issue when it came 
> up last year or if you have any advice on how I should proceed now. I 
> do have a folder named "log" in the directory I'm running the command 
> from.
>
> Thanks,
> Keji
> ---
> Morenikeji Adebayo
> Clinical Research Coordinator
> Interdisciplinary Affective Science Lab
> Massachusetts General Hospital
> Department of Psychiatric Neuroscience
>
> (p) 617.643.6347
> (f) 617.726.5760
> k...@nmr.mgh.harvard.edu 
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] funcroi-table-sess error, \"set: variable name must begin with a letter\"

[Douglas N Greve]

This is a different error:

ERROR: cannot find l_ant_cingulate_allVfix.roicfg


On 05/19/2015 02:55 PM, Joseph Andreano wrote:
> Hi Doug,
>
> I'm following up on a thread from a few months back, where we were
> experiencing difficulty with funcroi-table-sess.  (You can find the
> earlier thread here:
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg39326.html)
>
> I've attached the dng.log file you requested.  Please let me know if you
> can figure out the problem.
>
> Thanks,
> Joe Andreano
>
>
> _
>
> Joseph M. Andreano, PhD
> Postdoctoral Researcher
> Interdisciplinary Affective
> Science Laboratory
> Massachusetts General Hospital
> _
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] funcroi-table-sess error, "set: Variable name must begin with a letter"

[Douglas N Greve]

Is there a folder called "log" in the directly you are running it from? 
If not, try creating one. If so, then
run it with -debug as the first arg and send me the terminal output.

doug


On 08/19/2013 02:07 PM, Joseph Andreano wrote:
> Hi All,
>
> I'm trying to use funcroi-table-sess, but whenever I send this command:
>
> funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305
> -contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat
>
> I get this error:
>
> set: Variable name must begin with a letter
>
> So far as I can tell, all the variables in that command begin with a
> letter.  Any idea what the problem might be?
>
>
> _
>
> Joseph M. Andreano, PhD
> Postdoctoral Researcher
> Interdisciplinary Affective
> Science Laboratory
> Massachusetts General Hospital
> _
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] funcroi-table-sess error, "set: Variable name must begin with a letter"

[Douglas N Greve]

Hi Katie, can you run it with -debug as the first arg and send me the 
copious terminal output?
doug


On 08/30/2013 01:53 PM, Kathryn Devaney wrote:
> Hi Doug & Surfers,
>
> I'm having this same issue.  I'm running funcroi-table-sess on two
> analyses (lh and rh). There was no 'log' folder in my working directory,
> so I created it.  Everythingran fine for the lh, but when I try to run
> it in the rh I get
>
> set: Variable name must begin with a letter
>
> Here's the output of 'bugr' on my machine:
>
> -
>
> FREESURFER_HOME: /scratch/local/pkg/freesurfer/freesurfer-5.1.0
>
> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
>
> RedHat release: Fedora release 17 (Beefy Miracle)
>
> Kernel info: Linux 3.6.3-1.fc17.x86_64 x86_64
>
> -
>
> Let me know if you'd like me to send the terminal output of
> funcroi-table-sess -debug
>
> Thanks!
> Katie
>
>
>
> On 8/19/13 4:05 PM, Douglas N Greve wrote:
>> Is there a folder called "log" in the directly you are running it from?
>> If not, try creating one. If so, then
>> run it with -debug as the first arg and send me the terminal output.
>>
>> doug
>>
>>
>> On 08/19/2013 02:07 PM, Joseph Andreano wrote:
>>> Hi All,
>>>
>>> I'm trying to use funcroi-table-sess, but whenever I send this command:
>>>
>>> funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305
>>> -contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat
>>>
>>> I get this error:
>>>
>>> set: Variable name must begin with a letter
>>>
>>> So far as I can tell, all the variables in that command begin with a
>>> letter.  Any idea what the problem might be?
>>>
>>>
>>> _
>>>
>>> Joseph M. Andreano, PhD
>>> Postdoctoral Researcher
>>> Interdisciplinary Affective
>>>   Science Laboratory
>>> Massachusetts General Hospital
>>> _
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
> ___
> Freesurfer mailing list
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>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] funcroi-table-sess error, "set: Variable name must begin with a letter"

[Kathryn Devaney]

Hi Doug & Surfers,

I'm having this same issue.  I'm running funcroi-table-sess on two 
analyses (lh and rh). There was no 'log' folder in my working directory, 
so I created it.  Everythingran fine for the lh, but when I try to run 
it in the rh I get

set: Variable name must begin with a letter

Here's the output of 'bugr' on my machine:

-

FREESURFER_HOME: /scratch/local/pkg/freesurfer/freesurfer-5.1.0

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

RedHat release: Fedora release 17 (Beefy Miracle)

Kernel info: Linux 3.6.3-1.fc17.x86_64 x86_64

-

Let me know if you'd like me to send the terminal output of 
funcroi-table-sess -debug

Thanks!
Katie



On 8/19/13 4:05 PM, Douglas N Greve wrote:
> Is there a folder called "log" in the directly you are running it from?
> If not, try creating one. If so, then
> run it with -debug as the first arg and send me the terminal output.
>
> doug
>
>
> On 08/19/2013 02:07 PM, Joseph Andreano wrote:
>> Hi All,
>>
>> I'm trying to use funcroi-table-sess, but whenever I send this command:
>>
>> funcroi-table-sess -roi l_amyg_test -analysis habit_concat.mni305
>> -contrast neg1Vfix -sf subjects.lst -o l_amyg_neg1Vfix.dat
>>
>> I get this error:
>>
>> set: Variable name must begin with a letter
>>
>> So far as I can tell, all the variables in that command begin with a
>> letter.  Any idea what the problem might be?
>>
>>
>> _
>>
>> Joseph M. Andreano, PhD
>> Postdoctoral Researcher
>> Interdisciplinary Affective
>>  Science Laboratory
>> Massachusetts General Hospital
>> _
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
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