what's your cmd line? What version of FS?
Elif SIKOGLU wrote:
Hello I am trying to run the isxconcat-sess command. I keep getting the following error. It looks like it can not create this --mask-lh.mgh file, actually even DA1_coll250250-col250250 directory does not exist. Any ideas?
Thanks
/home/melifs/freesurfer/sessions/coll250250_study mri_vol2surf --mov /home/melifs/freesurfer/sessions/coll250250/DA1_coll250250/bold/coll250250///mask.nii --reg /home/melifs/freesurfer/sessions/coll250250/DA1_coll250250/bold/register.dat --trgsubject fsaverage --hemilh --interp nearest --noreshape --projfrac 0.5 --projfrac-avg 0 1 .2 --o ./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh srcvol = /home/melifs/freesurfer/sessions/coll250250/DA1_coll250250/bold/coll250250///mask.nii srcreg = /home/melifs/freesurfer/sessions/coll250250/DA1_coll250250/bold/register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /home/melifs/freesurfer/subjects/DA1/surf/lh.white Done reading source surface Reading thickness /home/melifs/freesurfer/subjects/DA1/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0 0 1 vol2surf_linear: nhits = 136215/136215 2 0.2 0 1 vol2surf_linear: nhits = 136215/136215 3 0.4 0 1 vol2surf_linear: nhits = 136215/136215 4 0.6 0 1 vol2surf_linear: nhits = 136215/136215 5 0.8 0 1 vol2surf_linear: nhits = 136215/136215 Done mapping volume to surface Number of source voxels hit = 8269 Reading source surface registration /home/melifs/freesurfer/subjects/DA1/surf/lh.sphere.reg Done loading source registration surface Reading target registration /home/melifs/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (DA1 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136215) Reverse Loop had 26091 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces mghWrite(./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh, -1): could not open file nSrc121 = 94106, nSrcLost = 0, nSrcMulti = 42109, MnSrcMultiHits = 2.27569 nTrg121 = 146432, nTrgMulti = 17410, MnTrgMultiHits = 2.49862 Writing to ./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh Dim: 163842 1 1
....
/home/melifs/freesurfer/sessions/coll250250_study mri_concat ./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/BC4_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/MB2_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/AJ_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/BG_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/MBA_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/GC_coll250250-coll250250/--mask-lh.mgh --o ./coll250250//lh.masks.nii mghRead(./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh, -1): could not open file ninputs = 7 Checking inputs ERROR: reading ./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh
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