date:20240310

Re: [Freesurfer] if: Expression Syntax - preproc-sess

2024-03-10 Thread Douglas N. Greve

Are you sure that you are using the new version that I gave you? It 
looks like the previous version. Also, it does not look like the entire 
terminal output.


On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote:


External Email - Use Caution

The entire terminal output is attached.
Thanks!

Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve 
 ha scritto:


entire terminal output


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Re: [Freesurfer] Trouble Project Surface Annotation to Volume

2024-03-10 Thread Douglas N. Greve

Hi Bram, try using mris_surfseg2vol. Look in the recon-all log file for 
an example usage

doug


On 3/10/2024 12:43 PM, Bram Diamond wrote:


External Email - Use Caution

Hello FreeSurfer Experts!

I’m having trouble projecting the Yeo 17n annotation to volume space. 
I’ve tried on FS v7.4.1 on Mac OS (14.3.1) and FS v7.3.2 on Linux (7.9).


I’ve tried the following two methods:

 1. aparc2aseg 

cd $FREESURFER_HOME/subjects/fsaverage/label

mri_aparc2aseg \

--s fsaverage \

--o Yeo2011_17Networks_N1000.mgz \

--annot Yeo2011_17Networks_N1000

 Output 

SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects

subject fsaverage

outvol Yeo2011_17Networks_N1000.mgz

useribbon 0

baseoffset 0

RipUnknown 0

Reading lh white surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white

Reading lh pial surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.pial

Loading lh annotations from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot


Have color table for lh white annotation

Building hash of lh white

Building hash of lh pial

Reading rh white surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.white

Reading rh pial surface

 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.pial

Loading rh annotations from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot


Have color table for rh white annotation

Building hash of rh white

Building hash of rh pial

Loading ribbon segmentation from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz


Loading aseg from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/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 (256)

  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 = 
332584


Used brute-force search on 0 voxels

Writing output aseg to Yeo2011_17Networks_N1000.mgz

error: mghWrite(Yeo2011_17Networks_N1000.mgz, -1): could not open file

#VMPC# mri_aparc2aseg VmPeak  0

mri_aparc2aseg done

 2. label2vol 

cd $FREESURFER_HOME/subjects/fsaverage/label

mri_label2vol \

--annot lh.Yeo2011_17Networks_N1000.annot \

--o lh.Yeo2011_17Networks_N1000.mgz \

--hemi lh \

--fill-ribbon \

--identity \

--subject fsaverage

 Output 

Number of labels: 0

Annot File:      lh.Yeo2011_17Networks_N1000.annot

Template Volume: (null)

Outut Volume: lh.Yeo2011_17Networks_N1000.mgz

Registration File: (null)

Fill Threshold: 0

Label Vox Vol:  1

ProjType:       (null)

ProjTypeId:     0

ProjStart:     0

ProjStop:       0

ProjDelta:     0.1

Subject: fsaverage

Hemi:     lh

UseNewASeg2Vol: 0

DoLabelStatVol 0

LabelCodeOffset 0

setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects

7.4.1

INFO: loading surface 
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white


nvertices = 163842

Reading thickness 
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.thickness


Loading annotations from lh.Yeo2011_17Networks_N1000.annot

annotidmax = 18

nlabels = 18

Loading /Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz

Mapping

error: mghWrite(lh.Yeo2011_17Networks_N1000.mgz, -1): could not open file



I’ve done this before, so I feel like I must be doing something wrong. 
Any ideas?


Cheers,

Bram

*Bram R. Diamond, MS*

Clinical Psychology Doctoral Candidate

Northwestern University Feinberg School of Medicine

Mesulam Center for Cognitive Neurology & Alzheimer’s Disease

300 E. Superior Street | Tarry 8 | Chicago, IL 60611

www.brain.northwestern.edu


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[Freesurfer] Trouble Project Surface Annotation to Volume

2024-03-10 Thread Bram Diamond

External Email - Use Caution

Hello FreeSurfer Experts!

I’m having trouble projecting the Yeo 17n annotation to volume space. I’ve 
tried on FS v7.4.1 on Mac OS (14.3.1) and FS v7.3.2 on Linux (7.9).

I’ve tried the following two methods:

 1. aparc2aseg 

cd $FREESURFER_HOME/subjects/fsaverage/label

mri_aparc2aseg \
--s fsaverage \
--o Yeo2011_17Networks_N1000.mgz \
--annot Yeo2011_17Networks_N1000

 Output 

SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects
subject fsaverage
outvol Yeo2011_17Networks_N1000.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface
 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white

Reading lh pial surface
 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.pial

Loading lh annotations from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/label/lh.Yeo2011_17Networks_N1000.annot
Have color table for lh white annotation

Building hash of lh white

Building hash of lh pial

Reading rh white surface
 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.white

Reading rh pial surface
 /Applications/freesurfer/7.4.1/subjects/fsaverage/surf/rh.pial

Loading rh annotations from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/label/rh.Yeo2011_17Networks_N1000.annot
Have color table for rh white annotation

Building hash of rh white

Building hash of rh pial
Loading ribbon segmentation from 
/Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz

Loading aseg from /Applications/freesurfer/7.4.1/subjects/fsaverage/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 (256)
  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 = 332584
Used brute-force search on 0 voxels
Writing output aseg to Yeo2011_17Networks_N1000.mgz
error: mghWrite(Yeo2011_17Networks_N1000.mgz, -1): could not open file
#VMPC# mri_aparc2aseg VmPeak  0
mri_aparc2aseg done

 2. label2vol 

cd $FREESURFER_HOME/subjects/fsaverage/label

mri_label2vol \
--annot lh.Yeo2011_17Networks_N1000.annot \
--o lh.Yeo2011_17Networks_N1000.mgz \
--hemi lh \
--fill-ribbon \
--identity \
--subject fsaverage

 Output 

Number of labels: 0
Annot File:  lh.Yeo2011_17Networks_N1000.annot
Template Volume: (null)
Outut Volume: lh.Yeo2011_17Networks_N1000.mgz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  fsaverage
Hemi: lh
UseNewASeg2Vol:  0
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects
7.4.1
  INFO: loading surface  
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.white
nvertices = 163842
Reading thickness 
/Applications/freesurfer/7.4.1/subjects/fsaverage/surf/lh.thickness
Loading annotations from lh.Yeo2011_17Networks_N1000.annot
annotidmax = 18
nlabels = 18
Loading /Applications/freesurfer/7.4.1/subjects/fsaverage/mri/ribbon.mgz
Mapping
error: mghWrite(lh.Yeo2011_17Networks_N1000.mgz, -1): could not open file



I’ve done this before, so I feel like I must be doing something wrong. Any 
ideas?

Cheers,
Bram

Bram R. Diamond, MS
Clinical Psychology Doctoral Candidate
Northwestern University Feinberg School of Medicine
Mesulam Center for Cognitive Neurology & Alzheimer’s Disease
300 E. Superior Street | Tarry 8 | Chicago, IL 60611
http://secure-web.cisco.com/1sXX_vt8lgAXmW5X0_GiTpKrZ-h1ollL1p35VMiSyPIOs3Zkz31Nf9_IKqecqpRdPddQjUJ96dIBSadhuULWM0wpsRq-rTetO_xJEA4sbT1C59KzMLS8kWtNa87zywhq16T_H0WeH0xW1LblyPfHt9dZkmwrjybw2OsSpkU94XM9KSSZM-X_4sh-uq2rT2J06DmiFb9Yu403AFJIfdWzhuzWnszpMsp198IUwPhSXnfs0CSb8GmSNdVlRuq5RqUg0eng4f7IoR1IiWNGCFnPM0ouuI5WaEp2f4-L4iJX2iKRzhqoE0bhUcPuK2TlBvub384TcqCKHPj7zY-iW38kraw/http%3A%2F%2Fwww.brain.northwestern.edu
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Re: [Freesurfer] if: Expression Syntax - preproc-sess

Re: [Freesurfer] Trouble Project Surface Annotation to Volume

[Freesurfer] Trouble Project Surface Annotation to Volume

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