Re: [Freesurfer] TRACULA - error

[Yendiki, Anastasia]

Hi Batool - Please send over your (actual and not made up :) config file and 
trac-all.log.

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rizvi, Batool 
[br2...@cumc.columbia.edu]
Sent: Tuesday, October 10, 2017 4:43 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA - error

Hi,
I’m running tracula using the following command:
(Note: I’m replacing actual paths with made up paths)

trac-all -prep -c /path/to/my/config.sh

And for some reason it stops running while working on the first subject 
(creates the folder for the first subject), with this error:

if: Expression Syntax.

It doesn’t show any errors before this line. The line before this one was 
copying over the bvecs file to the new path (cp /path/to/my/bvecs.txt 
path/to/dmri/dwi_orig.bvecs)

Is there something I’m doing wrong?

Thanks,
Batool


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[Freesurfer] TRACULA - error

[Rizvi, Batool]

Hi,
I'm running tracula using the following command:
(Note: I'm replacing actual paths with made up paths)

trac-all -prep -c /path/to/my/config.sh

And for some reason it stops running while working on the first subject 
(creates the folder for the first subject), with this error:

if: Expression Syntax.

It doesn't show any errors before this line. The line before this one was 
copying over the bvecs file to the new path (cp /path/to/my/bvecs.txt 
path/to/dmri/dwi_orig.bvecs)

Is there something I'm doing wrong?

Thanks,
Batool


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Re: [Freesurfer] Transformation between spaces

[Matt Glasser]

You would be running melodic from the command line.  If you have further
questions on CIFTI, the better place to ask would be the HCP-Users mailing
list:

https://www.humanconnectome.org/contact-us

Peace,

Matt.

From:   on behalf of Florence
Campana 
Reply-To:  Freesurfer support list 
Date:  Tuesday, October 10, 2017 at 12:12 PM
To:  Freesurfer support list 
Subject:  Re: [Freesurfer] Transformation between spaces

Hi Matt,

I follow-up on your suggestion of running MELODIC in surface. I am unsure
about the registration files that I should use (I guess that they should be
surface files?), notably for the Main Structural Images and the Standard
Space.
I am sorry if this sounds like a naive question.

Thank you very much,

Florence

2017-10-09 22:28 GMT-04:00 Matt Glasser :
> The latest version of melodic is compatible with CIFTI data (e.g. From the
> HCP).
> 
> Peace,
> 
> Matt.
> 
> From:   on behalf of Florence  Campana
> 
> Reply-To:  Freesurfer support list 
> Date:  Monday, October 9, 2017 at 9:25 PM
> To:  Freesurfer support list 
> Subject:  [Freesurfer] Transformation between spaces
> 
> Hi Matt,
> 
> Thank you for your quick input ; I did not try yet to use melodic, it seems
> indeed to be the most straightforward solution, I will try it, thank you
> again!
> 
> Florence
> 
> Le lundi 9 octobre 2017, Matt Glasser  a écrit :
>> I¹d note that you can run the group ICA on surface data in surface space
>> pretty easily using melodic, which would avoid the issue that Doug mentions.
>> 
>> Peace,
>> 
>> Matt.
>> 
>> From:   on behalf of Douglas Greve
>> 
>> Reply-To:  Freesurfer support list 
>> Date:  Monday, October 9, 2017 at 7:20 PM
>> To:  
>> Subject:  Re: [Freesurfer] Transformation between spaces
>> 
>> 
>>  
>> 
>> 
>>  
>>  
>> 
>> How did you get your ICA analysis into MNI305 (or MNI152) space?  You're ICA
>> intergroup comparisons will only be as good as that space -- how you get it
>> onto the surface from there is not so important. You can run recon-all on the
>> MNI152, sample the ICA maps onto the surface, then use the surface-based
>> registration to map it to fsaverage.
>>  
>>  
>>  
>> On 10/9/17 7:20 PM, Florence Campana wrote:
>>  
>>  
>>>  
>>> Dear freesurfer experts,
>>> 
>>>  
>>>  
>>> I ran a spatial ICA in volume and would like to visualize the components in
>>> surface in order to assess the overlap between the  independent components
>>> and my ROI (defined on surface). However after reading this paper,
>>> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am  concerned with
>>> transformations between the MNI 305 space and the surface space without
>>> totally understanding the nature of the distortions unfortunately. Would you
>>> mind explaining it briefly to me and let me know whether you think that the
>>> transformation of the components from the MNI305 space to the surface will
>>> lead to distorted results in the case of our spatial overlap estimates? (in
>>> which case I can define the ROI in volume and conduct all the analyses in
>>> volume).
>>>  
>>> 
>>>  
>>>  
>>> Thank you very much,
>>>  
>>> Florence Campana
>>>  
>>>  
>>>   
>>>  
>>> ___
>>> Freesurfer mailing list
>>> freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listi
>>> nfo/freesurfer
>>>  
>>  
>>  
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> 
> 

[Freesurfer] mri_aparc2aseg output file values

[Sims, Sara A]

Freesurfer people,

I have a label file that I want to make into a volume file only in the white 
matter to use in diffusion tractography.
I was told to use mri_aparc2aseg to put the labels onto the WM surface and make 
them into a volume. I made the label files into annotation files using the 
following commands:
mris_label2annot --ctab clut.2lhV1.ctab --s 100206 --h lh --l 
/data/user/snolin/subjects_reconall/100206/label/2_LH_V1.label --a 2V1
mris_label2annot --ctab clut.2rhV1.ctab --s 100206 --h rh --l 
/data/user/snolin/subjects_reconall/100206/label/2_RH_V1.label --a 2V1

These ran with no errors and made annotation files. Then I ran mri_aparc2aseg 
using the following command:
mri_aparc2aseg --s 100206 --annot 2V1 --new-ribbon

This is my log file:
SUBJECTS_DIR /data/user/snolin/subjects_reconall
subject 100206
outvol /data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface
 /data/user/snolin/subjects_reconall/100206/surf/lh.white

Reading lh pial surface
 /data/user/snolin/subjects_reconall/100206/surf/lh.pial

Loading lh annotations from 
/data/user/snolin/subjects_reconall/100206/label/lh.2V1.annot
reading colortable from annotation file...
colortable with 2 entries read (originally clut.2lhV1.ctab)

Reading rh white surface
 /data/user/snolin/subjects_reconall/100206/surf/rh.white

Reading rh pial surface
 /data/user/snolin/subjects_reconall/100206/surf/rh.pial

Loading rh annotations from 
/data/user/snolin/subjects_reconall/100206/label/rh.2V1.annot
reading colortable from annotation file...
colortable with 2 entries read (originally clut.2rhV1.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from 
/data/user/snolin/subjects_reconall/100206/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from /data/user/snolin/subjects_reconall/100206/mri/aseg.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
0.0   0.0   1.0  -128.0;
0.0  -1.0   0.0   128.0;
0.0   0.0   0.0   1.0;
-

Labeling Slice
  0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  19
 20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  39
 40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  59
 60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  79
 80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  99
100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119
120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139
140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159
160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199
200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219
220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1764
Used brute-force search on 0 voxels
Writing output aseg to 
/data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz

It creates the 2V1+aseg.mgz file and I tried opening it in freeview with the 
color lookup table that I used when I made it into an annotation file and its 
all black. Without the color lookup table it is all white.
Clicking around the values are 41, 0, or 2000 etc., but I can’t visually see 
anything. What have I done wrong here?

As I mentioned before, I just want to use these label file for diffusion 
tractography, so if I am heading down the wrong path, I would appreciate advice.

Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Platform: linux based cluster

Thank you!

Sara Sims

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Re: [Freesurfer] Descriptions of regions in Yeo 2011 Network atlases

[Mehta, Chintan]

Thank you Thomas!
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[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

[stdp82]

Thanks

In which contrast I must change "1" with "0.25"?
What is the rationale to use 0.25?


Sent from Virgilio Mobile


Il 10/10/2017, Douglas N Greve  ha scritto:

I don't understand what you mean by "where I should use"

I thought I looked through all those contrasts a few weeks ago, no?


On 10/10/2017 04:22 AM, std...@virgilio.it wrote:
> You have suggested to use
> 0 0 0 0 .25 .25 .25 .25
> to look the map where, considering the group differences, the covariate
> predicts the dependent variable (functional connectivity) in 4GV1.
>
> Below I'm reporting the contrast that I have used.
> Please could you check it and suggest correction?
> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please?
>
> Thanks
>
> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
> C15) group.effect.intercept
> 1 -1 0 0 0 0 0 0
> 1 0 -1 0 0 0 0 0
> 1 0 0 -1 0 0 0 0
> C16) group.effect.slope
>> 0 0 0 0 1 -1 0 0
>> 0 0 0 0 1 0 -1 0
>> 0 0 0 0 1 0 0 -1
>
>
>
>
>
>
>
> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>> Thank you very much.
>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>> Which are the contrast reported below that I should modify?
>>
>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>> C15) group.effect.intercept
>> 1 -1 0 0 0 0 0 0
>> 1 0 -1 0 0 0 0 0
>> 1 0 0 -1 0 0 0 0
>> C16) group.effect.slope
>> 0 0 0 0 1 -1 0 0
>> 0 0 0 0 1 0 -1 0
>> 0 0 0 0 1 0 0 -1
>
>> Messaggio originale
>> Da: "Douglas Greve" 
>> Data: 9-ott-2017 22.56
>> A: 
>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance
>>
>> I don't know what you are asking
>>
>>
>> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>>> Thank you very much.
>>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>>> Which are the contrast reported below that I should modify?
>>>
>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>>> C15) group.effect.intercept
>>> 1 -1 0 0 0 0 0 0
>>> 1 0 -1 0 0 0 0 0
>>> 1 0 0 -1 0 0 0 0
>>> C16) group.effect.slope
>>> 0 0 0 0 1 -1 0 0
>>> 0 0 0 0 1 0 -1 0
>>> 0 0 0 0 1 0 0 -1
>>>
>>>
 Messaggio originale
 Da: "Douglas Greve" 
 Data: 3-ott-2017 16.19
 A: 
 Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance

 probably you want 0 0 0 0 .25 .25 .25 .25



 On 10/3/17 10:10 AM, std...@virgilio.it wrote:
> Many thank for your response.
> Claryfing my question on point 3,
> When I look in group.effect.slope, the map show the group difference
>>> removing
> the effect of the covariate.
> Conversely, I would to obtain the map reporting only the effect of
>>> covariate
> on dependent variable (functional connectivity).
> Is possible to look on it?
> Regards
> Stefano
>
>
>> Messaggio originale
>> Da: "Douglas N Greve" 
>> Data: 2-ott-2017 16.58
>> A: 
>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance
>>
>>
>>
>> On 10/01/2017 05:08 PM, std...@virgilio.it wrote:
>>> Hi,
>>> on 4 groups, 1 covariate (4GV1)
>>>
>>> I run mri_glmfit using the following .mtx
>>>
>>> C1) 

Re: [Freesurfer] Transformation between spaces

[Florence Campana]

Hi Matt,

I follow-up on your suggestion of running MELODIC in surface. I am unsure
about the registration files that I should use (I guess that they should be
surface files?), notably for the Main Structural Images and the Standard
Space.
I am sorry if this sounds like a naive question.

Thank you very much,

Florence

2017-10-09 22:28 GMT-04:00 Matt Glasser :

> The latest version of melodic is compatible with CIFTI data (e.g. From the
> HCP).
>
> Peace,
>
> Matt.
>
> From:  on behalf of Florence
> Campana 
> Reply-To: Freesurfer support list 
> Date: Monday, October 9, 2017 at 9:25 PM
> To: Freesurfer support list 
> Subject: [Freesurfer] Transformation between spaces
>
> Hi Matt,
>
> Thank you for your quick input ; I did not try yet to use melodic, it
> seems indeed to be the most straightforward solution, I will try it, thank
> you again!
>
> Florence
>
> Le lundi 9 octobre 2017, Matt Glasser  a écrit :
>
>> I’d note that you can run the group ICA on surface data in surface space
>> pretty easily using melodic, which would avoid the issue that Doug mentions.
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of Douglas
>> Greve 
>> Reply-To: Freesurfer support list 
>> Date: Monday, October 9, 2017 at 7:20 PM
>> To: 
>> Subject: Re: [Freesurfer] Transformation between spaces
>>
>>
>> How did you get your ICA analysis into MNI305 (or MNI152) space?  You're
>> ICA intergroup comparisons will only be as good as that space -- how you
>> get it onto the surface from there is not so important. You can run
>> recon-all on the MNI152, sample the ICA maps onto the surface, then use the
>> surface-based registration to map it to fsaverage.
>>
>> On 10/9/17 7:20 PM, Florence Campana wrote:
>>
>> Dear freesurfer experts,
>>
>> I ran a spatial ICA in volume and would like to visualize the components
>> in surface in order to assess the overlap between the  independent
>> components and my ROI (defined on surface). However after reading this
>> paper, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2862732/, I am
>>  concerned with transformations between the MNI 305 space and the surface
>> space without totally understanding the nature of the distortions
>> unfortunately. Would you mind explaining it briefly to me and let me know
>> whether you think that the transformation of the components from the MNI305
>> space to the surface will lead to distorted results in the case of our
>> spatial overlap estimates? (in which case I can define the ROI in volume
>> and conduct all the analyses in volume).
>>
>> Thank you very much,
>> Florence Campana
>>
>>
>> ___
>> Freesurfer mailing 
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>>
>>
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>> intended only for the person to whom it is addressed. If you believe this
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>> information, please contact the Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error but does not contain patient information, please contact the
>> sender and properly dispose of the e-mail.
>>
> ___ Freesurfer mailing list
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
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[Freesurfer] Postdoctoral Fellowship at Mayo Clinic in Imaging Biomarker Development

[Senjem, Matthew L., M.S.]

Postdoctoral Fellowship at Mayo Clinic in Imaging Biomarker Development

Position Summary: A Research Fellow is being sought in the Department of 
Radiology at Mayo Clinic in Rochester, Minnesota.
The focus of the research for this position will be on multimodal imaging 
changes (DTI, ASL, fMRI) associated with cerebrovascular disease, dementia, and 
brain resilience.
Successful candidates should have background knowledge in mathematics, 
electrical engineering, computer science, biomedical engineering, or statistics.
Applicants should be able to demonstrate good communication skills through 
publications in peer-reviewed publications.
The position is currently for three years.

If interested, please send your CV to Prashanthi Vemuri, PhD 
(vemuri.prashan...@mayo.edu).

The complete posting is available here - 
http://www.mayo-clinic-jobs.com/job/Rochester-Research-Fellow-Radiology-Job-MN-55901/431010600/


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Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

[Douglas N Greve]

I don't understand what you mean by "where I should use"

I thought I looked through all those contrasts a few weeks ago, no?


On 10/10/2017 04:22 AM, std...@virgilio.it wrote:
> You have suggested to use
> 0 0 0 0 .25 .25 .25 .25
> to look the map where, considering the group differences, the covariate
> predicts the dependent variable (functional connectivity) in 4GV1.
>
> Below I'm reporting the contrast that I have used.
> Please could you check it and suggest correction?
> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please?
>
> Thanks
>
> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
> C15) group.effect.intercept
> 1 -1 0 0 0 0 0 0
> 1 0 -1 0 0 0 0 0
> 1 0 0 -1 0 0 0 0
> C16) group.effect.slope
>> 0 0 0 0 1 -1 0 0
>> 0 0 0 0 1 0 -1 0
>> 0 0 0 0 1 0 0 -1
>
>
>
>
>
>
>
> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>> Thank you very much.
>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>> Which are the contrast reported below that I should modify?
>>
>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>> C15) group.effect.intercept
>> 1 -1 0 0 0 0 0 0
>> 1 0 -1 0 0 0 0 0
>> 1 0 0 -1 0 0 0 0
>> C16) group.effect.slope
>> 0 0 0 0 1 -1 0 0
>> 0 0 0 0 1 0 -1 0
>> 0 0 0 0 1 0 0 -1
>
>> Messaggio originale
>> Da: "Douglas Greve" 
>> Data: 9-ott-2017 22.56
>> A: 
>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance
>>
>> I don't know what you are asking
>>
>>
>> On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>>> Thank you very much.
>>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>>> Which are the contrast reported below that I should modify?
>>>
>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>>> C15) group.effect.intercept
>>> 1 -1 0 0 0 0 0 0
>>> 1 0 -1 0 0 0 0 0
>>> 1 0 0 -1 0 0 0 0
>>> C16) group.effect.slope
>>> 0 0 0 0 1 -1 0 0
>>> 0 0 0 0 1 0 -1 0
>>> 0 0 0 0 1 0 0 -1
>>>
>>>
 Messaggio originale
 Da: "Douglas Greve" 
 Data: 3-ott-2017 16.19
 A: 
 Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance

 probably you want 0 0 0 0 .25 .25 .25 .25



 On 10/3/17 10:10 AM, std...@virgilio.it wrote:
> Many thank for your response.
> Claryfing my question on point 3,
> When I look in group.effect.slope, the map show the group difference
>>> removing
> the effect of the covariate.
> Conversely, I would to obtain the map reporting only the effect of
>>> covariate
> on dependent variable (functional connectivity).
> Is possible to look on it?
> Regards
> Stefano
>
>
>> Messaggio originale
>> Da: "Douglas N Greve" 
>> Data: 2-ott-2017 16.58
>> A: 
>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance
>>
>>
>>
>> On 10/01/2017 05:08 PM, std...@virgilio.it wrote:
>>> Hi,
>>> on 4 groups, 1 covariate (4GV1)
>>>
>>> I run mri_glmfit using the following .mtx
>>>
>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>>> C6) 

Re: [Freesurfer] Original dimension

[Fereshte]

I found out the problem, thanks for your attention.
Regards

On Tue, Oct 10, 2017 at 12:32 AM Douglas Greve 
wrote:

> what is the dimension of the rawavg.mgz? what is the dimension of the
> output? What is the terminal output?
>
> On 10/8/17 1:51 AM, Fereshte wrote:
>
> Dear Experts,
> I've run " mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o
> aseg-in-rawavg.mgz --regheader aseg.mgz" as explained, however i can't see
> any changes in dimension in comparision to the the predefined aseg.mgz. I'd
> appreciate your help with it.
> Thanks for your attention. I'm looking forward to your reply.
>
>
>
> On Wed, Oct 4, 2017 at 5:01 PM, Douglas Greve 
> wrote:
>
>> This is a standard operation in FS to change the volume to 256^3, 1mm^3.
>> If you need to get the data back into the native space, see
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
>>
>> On 10/4/17 3:31 AM, Fereshte wrote:
>>
>> Dear Experts,
>> I've made some volumes from aseg.mgz using mri_binarize and then used
>> mri_convert to make nii files. But when i open these files using Mricro i
>> see the original dimension of the image has changed ( 181,217,181 to
>> 256,256,256). I have no idea what the problem is. I'd appreciate your help.
>> Many thanks in advance
>> Best
>>
>>
>> ___
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>>
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>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
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>> dispose of the e-mail.
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>
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> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] Fwd: Tracula dpath error

[Yendiki, Anastasia]

Hi Anna - There was no method for intra-subject (diffusion to structural) 
registration selected in your config file, so some steps were skipped. Change 
the 0 to a 1 in this line: "set doregbbr = 0" and then rerun the preprocessing 
(you can skip the steps before the intra-subject registration if you want).

Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anna Varghese 
[annavarghes...@gmail.com]
Sent: Tuesday, October 10, 2017 12:28 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Fwd: Tracula dpath error

Dear all,


I am unable to get the dpath folder after the running the "trac-all path " 
step, although it shows an information on the terminal as "trac-paths finished 
without error".

Earlier, I had experienced an error with "trac-all bedp" but I ran it locally 
by directly using the "bedpostx " command. A dmri.bedpostX folder 
with all the files have been created . Following this, I encountered the above 
mentioned problem for pathway reconstruction. I have attached the config file 
and trac-all.log file.

Would appreciate any help.

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addressed. If you believe this e-mail was sent to you in error and the e-mail
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[Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance

[stdp82]

You have suggested to use
0 0 0 0 .25 .25 .25 .25
to look the map where, considering the group differences, the covariate 
predicts the dependent variable (functional connectivity) in 4GV1.

Below I'm reporting the contrast that I have used. 
Please could you check it and suggest correction?
Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please?

Thanks

C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
C15) group.effect.intercept
1 -1 0 0 0 0 0 0
1 0 -1 0 0 0 0 0
1 0 0 -1 0 0 0 0
C16) group.effect.slope
> 0 0 0 0 1 -1 0 0
> 0 0 0 0 1 0 -1 0
> 0 0 0 0 1 0 0 -1








On 10/6/17 9:24 AM, std...@virgilio.it wrote:
> Thank you very much.
> Where I should put 0 0 0 0 .25 .25 .25 .25?
> Which are the contrast reported below that I should modify?
>
> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
> C15) group.effect.intercept
> 1 -1 0 0 0 0 0 0
> 1 0 -1 0 0 0 0 0
> 1 0 0 -1 0 0 0 0
> C16) group.effect.slope
> 0 0 0 0 1 -1 0 0
> 0 0 0 0 1 0 -1 0
> 0 0 0 0 1 0 0 -1


>Messaggio originale
>Da: "Douglas Greve" 
>Data: 9-ott-2017 22.56
>A: 
>Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance
>
>I don't know what you are asking
>
>
>On 10/6/17 9:24 AM, std...@virgilio.it wrote:
>> Thank you very much.
>> Where I should put 0 0 0 0 .25 .25 .25 .25?
>> Which are the contrast reported below that I should modify?
>>
>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1
>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0
>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5
>> C15) group.effect.intercept
>> 1 -1 0 0 0 0 0 0
>> 1 0 -1 0 0 0 0 0
>> 1 0 0 -1 0 0 0 0
>> C16) group.effect.slope
>> 0 0 0 0 1 -1 0 0
>> 0 0 0 0 1 0 -1 0
>> 0 0 0 0 1 0 0 -1
>>
>>
>>> Messaggio originale
>>> Da: "Douglas Greve" 
>>> Data: 3-ott-2017 16.19
>>> A: 
>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance
>>>
>>> probably you want 0 0 0 0 .25 .25 .25 .25
>>>
>>>
>>>
>>> On 10/3/17 10:10 AM, std...@virgilio.it wrote:
 Many thank for your response.
 Claryfing my question on point 3,
 When I look in group.effect.slope, the map show the group difference
>> removing
 the effect of the covariate.
 Conversely, I would to obtain the map reporting only the effect of
>> covariate
 on dependent variable (functional connectivity).
 Is possible to look on it?
 Regards
 Stefano


> Messaggio originale
> Da: "Douglas N Greve" 
> Data: 2-ott-2017 16.58
> A: 
> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance
>
>
>
> On 10/01/2017 05:08 PM, std...@virgilio.it wrote:
>> Hi,
>> on 4 groups, 1 covariate (4GV1)
>>
>> I run mri_glmfit using the following .mtx
>>
>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0
>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0
>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0
>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0
>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0
>> C6) gr1-gr4_slope 0 0 0 0 1 0 -1 0
> should be
>
> 0 0 0 0 1 0 0 -1
>
>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0
>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0
>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0
>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1
>> C11) gr3-gr4_intercept  0 0 1 -1 0 0 0 0
>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1
>>